Publications

George Tseng

Kinzy TG, Starr TK, Tseng GC, Ho YY. Meta-analytic framework for modeling genetic coexpression dynamics. Stat Appl Genet Mol Biol. 2019 Feb 9;18(1): doi: 10.1515/sagmb-2017-0052. PubMed PMID: 30735484.
Yu YP, Liu P, Nelson J, Hamilton RL, Bhargava R, Michalopoulos G, Chen Q, Zhang J, Ma D, Pennathur A, Luketich J, Nalesnik M, Tseng G, Luo JH. Identification of recurrent fusion genes across multiple cancer types. Sci Rep. 2019 Jan 31;9(1):1074. doi: 10.1038/s41598-019-38550-6. PubMed PMID: 30705370; PMCID: PMC6355770.
Grabosch S, Bulatovic M, Zeng F, Ma T, Zhang L, Ross M, Brozick J, Fang Y, Tseng G, Kim E, Gambotto A, Elishaev E, P Edwards R, Vlad AM. Cisplatin-induced immune modulation in ovarian cancer mouse models with distinct inflammation profiles. Oncogene. 2019 Mar;38(13):2380-2393. doi: 10.1038/s41388-018-0581-9. PubMed PMID: 30518877; PMCID: PMC6440870.
Andersen CL, Boisen MM, Sikora MJ, Ma T, Tseng G, Suryawanshi S, Vlad A, Elishaev E, Edwards RP, Oesterreich S. The Evolution of Estrogen Receptor Signaling in the Progression of Endometriosis to Endometriosis-Associated Ovarian Cancer. Horm Cancer. 2018 Dec;9(6):399-407. doi: 10.1007/s12672-018-0350-9. PubMed PMID: 30302736.
Ma T, Huo Z, Kuo A, Zhu L, Fang Z, Zeng X, Lin CW, Liu S, Wang L, Liu P, Rahman T, Chang LC, Kim S, Li J, Park Y, Song C, Oesterreich S, Sibille E, Tseng GC. MetaOmics: analysis pipeline and browser-based software suite for transcriptomic meta-analysis. Bioinformatics. 2019 May 1;35(9):1597-1599. doi: 10.1093/bioinformatics/bty825. PubMed PMID: 30304367; PMCID: PMC6499246.
Tasdemir N, Bossart EA, Li Z, Zhu L, Sikora MJ, Levine KM, Jacobsen BM, Tseng GC, Davidson NE, Oesterreich S. Comprehensive Phenotypic Characterization of Human Invasive Lobular Carcinoma Cell Lines in 2D and 3D Cultures. Cancer Res. 2018 Nov 1;78(21):6209-6222. doi: 10.1158/0008-5472.CAN-18-1416. PubMed PMID: 30228172; PMCID: PMC6507416.
Fang Z, Ma T, Tang G, Zhu L, Yan Q, Wang T, Celedón JC, Chen W, Tseng GC. Bayesian integrative model for multi-omics data with missingness. Bioinformatics. 2018 Nov 15;34(22):3801-3808. doi: 10.1093/bioinformatics/bty775. PubMed PMID: 30184058; PMCID: PMC6223369.
Tsagianni A, Mars WM, Bhushan B, Bowen WC, Orr A, Stoops J, Paranjpe S, Tseng GC, Liu S, Michalopoulos GK. Combined Systemic Disruption of MET and Epidermal Growth Factor Receptor Signaling Causes Liver Failure in Normal Mice. Am J Pathol. 2018 Oct;188(10):2223-2235. doi: 10.1016/j.ajpath.2018.06.009. PubMed PMID: 30031724; PMCID: PMC6168971.
Varešlija D, Priedigkeit N, Fagan A, Purcell S, Cosgrove N, O'Halloran PJ, Ward E, Cocchiglia S, Hartmaier R, Castro CA, Zhu L, Tseng GC, Lucas PC, Puhalla SL, Brufsky AM, Hamilton RL, Mathew A, Leone JP, Basudan A, Hudson L, Dwyer R, Das S, O'Connor DP, Buckley PG, Farrell M, Hill ADK, Oesterreich S, Lee AV, Young LS. Transcriptome Characterization of Matched Primary Breast and Brain Metastatic Tumors to Detect Novel Actionable Targets. J Natl Cancer Inst. 2019 Apr 1;111(4):388-398. doi: 10.1093/jnci/djy110. PubMed PMID: 29961873; PMCID: PMC6449168.
Cahill KM, Huo Z, Tseng GC, Logan RW, Seney ML. Improved identification of concordant and discordant gene expression signatures using an updated rank-rank hypergeometric overlap approach. Sci Rep. 2018 Jun 25;8(1):9588. doi: 10.1038/s41598-018-27903-2. PubMed PMID: 29942049; PMCID: PMC6018631.
Du T, Zhu L, Levine KM, Tasdemir N, Lee AV, Vignali DAA, Houten BV, Tseng GC, Oesterreich S. Invasive lobular and ductal breast carcinoma differ in immune response, protein translation efficiency and metabolism. Sci Rep. 2018 May 8;8(1):7205. doi: 10.1038/s41598-018-25357-0. PubMed PMID: 29739984; PMCID: PMC5940770.
Kim S, Kang D, Huo Z, Park Y, Tseng GC. Meta-analytic principal component analysis in integrative omics application. Bioinformatics. 2018 Apr 15;34(8):1321-1328. doi: 10.1093/bioinformatics/btx765. PubMed PMID: 29186328; PMCID: PMC5905607.
Huo Z, Tseng G. Integrative Sparse K-Means With Overlapping Group Lasso in Genomic Applications for Disease Subtype Discovery. Ann Appl Stat. 2017 Jun;11(2):1011-1039. doi: 10.1214/17-AOAS1033. PubMed PMID: 28959370; PMCID: PMC5613668.
Ma T, Liang F, Tseng G. Biomarker detection and categorization in ribonucleic acid sequencing meta-analysis using Bayesian hierarchical models. J R Stat Soc Ser C Appl Stat. 2017 Aug;66(4):847-867. doi: 10.1111/rssc.12199. PubMed PMID: 28785119; PMCID: PMC5543999.
Ma T, Liang F, Oesterreich S, Tseng GC. A Joint Bayesian Model for Integrating Microarray and RNA Sequencing Transcriptomic Data. J Comput Biol. 2017 Jul;24(7):647-662. doi: 10.1089/cmb.2017.0056. PubMed PMID: 28541721; PMCID: PMC5510692.
Grabosch S, Tseng G, Edwards RP, Lankes HA, Moore K, Odunsi K, Vlad A, Ma T, Strange M, Brozick J, Lugade A, Omilian A, Bshara W, Stuckey AR, Walker JL, Birrer M. Multiplex profiling identifies distinct local and systemic alterations during intraperitoneal chemotherapy for ovarian cancer: An NRG Oncology/Gynecologic Oncology Group Study. Gynecol Oncol. 2017 Jul;146(1):137-145. doi: 10.1016/j.ygyno.2017.04.008. PubMed PMID: 28483269; PMCID: PMC5705948.
Chen ZH, Yu YP, Zuo ZH, Nelson JB, Michalopoulos GK, Monga S, Liu S, Tseng G, Luo JH. Targeting genomic rearrangements in tumor cells through Cas9-mediated insertion of a suicide gene. Nat Biotechnol. 2017 Jun;35(6):543-550. doi: 10.1038/nbt.3843. PubMed PMID: 28459452; PMCID: PMC5462845.
Wang L, Liu S, Ding Y, Yuan SS, Ho YY, Tseng GC. Meta-analytic framework for liquid association. Bioinformatics. 2017 Jul 15;33(14):2140-2147. doi: 10.1093/bioinformatics/btx138. PubMed PMID: 28334340; PMCID: PMC6044323.
Chen ZH, Yu YP, Tao J, Liu S, Tseng G, Nalesnik M, Hamilton R, Bhargava R, Nelson JB, Pennathur A, Monga SP, Luketich JD, Michalopoulos GK, Luo JH. MAN2A1-FER Fusion Gene Is Expressed by Human Liver and Other Tumor Types and Has Oncogenic Activity in Mice. Gastroenterology. 2017 Oct;153(4):1120-1132.e15. doi: 10.1053/j.gastro.2016.12.036. PubMed PMID: 28245430; PMCID: PMC5572118.
Andersen CL, Sikora MJ, Boisen MM, Ma T, Christie A, Tseng G, Park Y, Luthra S, Chandran U, Haluska P, Mantia-Smaldone GM, Odunsi K, McLean K, Lee AV, Elishaev E, Edwards RP, Oesterreich S. Active Estrogen Receptor-alpha Signaling in Ovarian Cancer Models and Clinical Specimens. Clin Cancer Res. 2017 Jul 15;23(14):3802-3812. doi: 10.1158/1078-0432.CCR-16-1501. PubMed PMID: 28073843; PMCID: PMC5503796.
Zhu L, Ding Y, Chen CY, Wang L, Huo Z, Kim S, Sotiriou C, Oesterreich S, Tseng GC. MetaDCN: meta-analysis framework for differential co-expression network detection with an application in breast cancer. Bioinformatics. 2017 Apr 15;33(8):1121-1129. doi: 10.1093/bioinformatics/btw788. PubMed PMID: 28031185; PMCID: PMC6041767.
Paranjpe S, Bowen WC, Mars WM, Orr A, Haynes MM, DeFrances MC, Liu S, Tseng GC, Tsagianni A, Michalopoulos GK. Combined systemic elimination of MET and epidermal growth factor receptor signaling completely abolishes liver regeneration and leads to liver decompensation. Hepatology. 2016 Nov;64(5):1711-1724. doi: 10.1002/hep.28721. PubMed PMID: 27397846; PMCID: PMC5074871.
Kim S, Oesterreich S, Kim S, Park Y, Tseng GC. Integrative clustering of multi-level omics data for disease subtype discovery using sequential double regularization. Biostatistics. 2017 Jan;18(1):165-179. doi: 10.1093/biostatistics/kxw039. PubMed PMID: 27549122; PMCID: PMC5255053.
Richardson S, Tseng GC, Sun W. Statistical Methods in Integrative Genomics. Annu Rev Stat Appl. 2016 Jun;3181-209. doi: 10.1146/annurev-statistics-041715-033506. PubMed PMID: 27482531; PMCID: PMC4963036.
Huo Z, Ding Y, Liu S, Oesterreich S, Tseng G. Meta-analytic framework for sparse K-means to identify disease subtypes in multiple transcriptomic studies. J Am Stat Assoc. 2016;111(513):27-42. doi: 10.1080/01621459.2015.1086354. PubMed PMID: 27330233; PMCID: PMC4908837.
Kim S, Lin CW, Tseng GC. MetaKTSP: a meta-analytic top scoring pair method for robust cross-study validation of omics prediction analysis. Bioinformatics. 2016 Jul 1;32(13):1966-73. doi: 10.1093/bioinformatics/btw115. PubMed PMID: 27153719; PMCID: PMC6280887.
Delgado E, Boisen MM, Laskey R, Chen R, Song C, Sallit J, Yochum ZA, Andersen CL, Sikora MJ, Wagner J, Safe S, Elishaev E, Lee A, Edwards RP, Haluska P, Tseng G, Schurdak M, Oesterreich S. High expression of orphan nuclear receptor NR4A1 in a subset of ovarian tumors with worse outcome. Gynecol Oncol. 2016 May;141(2):348-356. doi: 10.1016/j.ygyno.2016.02.030. PubMed PMID: 26946093; PMCID: PMC5154956.
Chang LC, Li B, Fang Z, Vrieze S, McGue M, Iacono WG, Tseng GC, Chen W. A computational method for genotype calling in family-based sequencing data. BMC Bioinformatics. 2016 Jan 16;1737. doi: 10.1186/s12859-016-0880-5. PubMed PMID: 26772743; PMCID: PMC4715317.
Begum F, Sharker MH, Sherman SL, Tseng GC, Feingold E. Regionally Smoothed Meta-Analysis Methods for GWAS Datasets. Genet Epidemiol. 2016 Feb;40(2):154-60. doi: 10.1002/gepi.21949. PubMed PMID: 26707090; PMCID: PMC4724289.
Liu S, Tsai WH, Ding Y, Chen R, Fang Z, Huo Z, Kim S, Ma T, Chang TY, Priedigkeit NM, Lee AV, Luo J, Wang HW, Chung IF, Tseng GC. Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data. Nucleic Acids Res. 2016 Mar 18;44(5):e47. doi: 10.1093/nar/gkv1234. PubMed PMID: 26582927; PMCID: PMC4797269.
Kim S, Herazo-Maya JD, Kang DD, Juan-Guardela BM, Tedrow J, Martinez FJ, Sciurba FC, Tseng GC, Kaminski N. Integrative phenotyping framework (iPF): integrative clustering of multiple omics data identifies novel lung disease subphenotypes. BMC Genomics. 2015 Nov 11;16924. doi: 10.1186/s12864-015-2170-4. PubMed PMID: 26560100; PMCID: PMC4642618.
Yu YP, Liu S, Huo Z, Martin A, Nelson JB, Tseng GC, Luo JH. Genomic Copy Number Variations in the Genomes of Leukocytes Predict Prostate Cancer Clinical Outcomes. PLoS One. 2015;10(8):e0135982. doi: 10.1371/journal.pone.0135982. PubMed PMID: 26295840; PMCID: PMC4546524.
Katz TA, Liao SG, Palmieri VJ, Dearth RK, Pathiraja TN, Huo Z, Shaw P, Small S, Davidson NE, Peters DG, Tseng GC, Oesterreich S, Lee AV. Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition. Cancer Prev Res (Phila). 2015 Oct;8(10):1000-9. doi: 10.1158/1940-6207.CAPR-15-0178. PubMed PMID: 26290394; PMCID: PMC4677681.
Liao S, Hartmaier RJ, McGuire KP, Puhalla SL, Luthra S, Chandran UR, Ma T, Bhargava R, Modugno F, Davidson NE, Benz S, Lee AV, Tseng GC, Oesterreich S. The molecular landscape of premenopausal breast cancer. Breast Cancer Res. 2015 Aug 7;17104. doi: 10.1186/s13058-015-0618-8. PubMed PMID: 26251034; PMCID: PMC4531812.
Mony JT, Zhang L, Ma T, Grabosch S, Tirodkar TS, Brozick J, Tseng G, Elishaev E, Edwards RP, Huang X, Vlad AM. Anti-PD-L1 prolongs survival and triggers T cell but not humoral anti-tumor immune responses in a human MUC1-expressing preclinical ovarian cancer model. Cancer Immunol Immunother. 2015 Sep;64(9):1095-108. doi: 10.1007/s00262-015-1712-6. PubMed PMID: 25998800; PMCID: PMC4545381.
Luo JH, Liu S, Zuo ZH, Chen R, Tseng GC, Yu YP. Discovery and Classification of Fusion Transcripts in Prostate Cancer and Normal Prostate Tissue. Am J Pathol. 2015 Jul;185(7):1834-45. doi: 10.1016/j.ajpath.2015.03.008. PubMed PMID: 25963990; PMCID: PMC4483459.
Zuo ZH, Yu YP, Ding Y, Liu S, Martin A, Tseng G, Luo JH. Oncogenic Activity of miR-650 in Prostate Cancer Is Mediated by Suppression of CSR1 Expression. Am J Pathol. 2015 Jul;185(7):1991-9. doi: 10.1016/j.ajpath.2015.03.015. PubMed PMID: 25956032; PMCID: PMC4484220.

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