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Metabolites associated with walking ability among the oldest old from the CHS All Stars study.

Marron MM, Wendell SG, Boudreau RM, Clish CB, Santanasto AJ, Tseng GC, Zmuda JM, Newman AB.

J Gerontol A Biol Sci Med Sci. 2020 Jan 23. pii: glaa030. doi: 10.1093/gerona/glaa030. [Epub ahead of print]


Metastatic breast cancers have reduced immune cell recruitment but harbor increased macrophages relative to their matched primary tumors.

Zhu L, Narloch JL, Onkar S, Joy M, Broadwater G, Luedke C, Hall A, Kim R, Pogue-Geile K, Sammons S, Nayyar N, Chukwueke U, Brastianos PK, Anders CK, Soloff AC, Vignali DAA, Tseng GC, Emens LA, Lucas PC, Blackwell KL, Oesterreich S, Lee AV.

J Immunother Cancer. 2019 Oct 18;7(1):265. doi: 10.1186/s40425-019-0755-1.


Immunological evaluation of a novel HLA-A2 restricted phosphopeptide of tumor associated Antigen, TRAP1, on cancer therapy.

Lin MH, Shen KY, Liu BS, Chen IH, Sher YP, Tseng GC, Liu SJ, Sung WC.

Vaccine X. 2019 Mar 11;1:100017. doi: 10.1016/j.jvacx.2019.100017. eCollection 2019 Apr 11.


Metabolites Associated with Vigor to Frailty Among Community-Dwelling Older Black Men.

Marron MM, Harris TB, Boudreau RM, Clish CB, Moore SC, Murphy RA, Murthy VL, Sanders JL, Shah RV, Tseng GC, Wendell SG, Zmuda JM, Newman AB.

Metabolites. 2019 Apr 30;9(5). pii: E83. doi: 10.3390/metabo9050083.


Meta-analytic framework for modeling genetic coexpression dynamics.

Kinzy TG, Starr TK, Tseng GC, Ho YY.

Stat Appl Genet Mol Biol. 2019 Feb 9;18(1). pii: /j/sagmb.2019.18.issue-1/sagmb-2017-0052/sagmb-2017-0052.xml. doi: 10.1515/sagmb-2017-0052.


MetaOmics: analysis pipeline and browser-based software suite for transcriptomic meta-analysis.

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.

Bioinformatics. 2019 May 1;35(9):1597-1599. doi: 10.1093/bioinformatics/bty825.


Comprehensive Phenotypic Characterization of Human Invasive Lobular Carcinoma Cell Lines in 2D and 3D Cultures.

Tasdemir N, Bossart EA, Li Z, Zhu L, Sikora MJ, Levine KM, Jacobsen BM, Tseng GC, Davidson NE, Oesterreich S.

Cancer Res. 2018 Nov 1;78(21):6209-6222. doi: 10.1158/0008-5472.CAN-18-1416. Epub 2018 Sep 18.


Bayesian integrative model for multi-omics data with missingness.

Fang Z, Ma T, Tang G, Zhu L, Yan Q, Wang T, Celedón JC, Chen W, Tseng GC.

Bioinformatics. 2018 Nov 15;34(22):3801-3808. doi: 10.1093/bioinformatics/bty775.


Combined Systemic Disruption of MET and Epidermal Growth Factor Receptor Signaling Causes Liver Failure in Normal Mice.

Tsagianni A, Mars WM, Bhushan B, Bowen WC, Orr A, Stoops J, Paranjpe S, Tseng GC, Liu S, Michalopoulos GK.

Am J Pathol. 2018 Oct;188(10):2223-2235. doi: 10.1016/j.ajpath.2018.06.009. Epub 2018 Jul 20.


Transcriptome Characterization of Matched Primary Breast and Brain Metastatic Tumors to Detect Novel Actionable Targets.

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.

J Natl Cancer Inst. 2019 Apr 1;111(4):388-398. doi: 10.1093/jnci/djy110.


Improved identification of concordant and discordant gene expression signatures using an updated rank-rank hypergeometric overlap approach.

Cahill KM, Huo Z, Tseng GC, Logan RW, Seney ML.

Sci Rep. 2018 Jun 25;8(1):9588. doi: 10.1038/s41598-018-27903-2.


Invasive lobular and ductal breast carcinoma differ in immune response, protein translation efficiency and metabolism.

Du T, Zhu L, Levine KM, Tasdemir N, Lee AV, Vignali DAA, Houten BV, Tseng GC, Oesterreich S.

Sci Rep. 2018 May 8;8(1):7205. doi: 10.1038/s41598-018-25357-0.


Meta-analytic principal component analysis in integrative omics application.

Kim S, Kang D, Huo Z, Park Y, Tseng GC.

Bioinformatics. 2018 Apr 15;34(8):1321-1328. doi: 10.1093/bioinformatics/btx765.


Sustained Molecular Pathology Across Episodes and Remission in Major Depressive Disorder.

Scifo E, Pabba M, Kapadia F, Ma T, Lewis DA, Tseng GC, Sibille E.

Biol Psychiatry. 2018 Jan 1;83(1):81-89. doi: 10.1016/j.biopsych.2017.08.008. Epub 2017 Aug 18.


Resilient protein co-expression network in male orbitofrontal cortex layer 2/3 during human aging.

Pabba M, Scifo E, Kapadia F, Nikolova YS, Ma T, Mechawar N, Tseng GC, Sibille E.

Neurobiol Aging. 2017 Oct;58:180-190. doi: 10.1016/j.neurobiolaging.2017.06.023. Epub 2017 Jul 5.


Comparing the effects of afatinib with gefitinib or Erlotinib in patients with advanced-stage lung adenocarcinoma harboring non-classical epidermal growth factor receptor mutations.

Shen YC, Tseng GC, Tu CY, Chen WC, Liao WC, Chen WC, Li CH, Chen HJ, Hsia TC.

Lung Cancer. 2017 Aug;110:56-62. doi: 10.1016/j.lungcan.2017.06.007. Epub 2017 Jun 13.


Age-Related Gene Expression in the Frontal Cortex Suggests Synaptic Function Changes in Specific Inhibitory Neuron Subtypes.

French L, Ma T, Oh H, Tseng GC, Sibille E.

Front Aging Neurosci. 2017 May 29;9:162. doi: 10.3389/fnagi.2017.00162. eCollection 2017.


A Joint Bayesian Model for Integrating Microarray and RNA Sequencing Transcriptomic Data.

Ma T, Liang F, Oesterreich S, Tseng GC.

J Comput Biol. 2017 Jul;24(7):647-662. doi: 10.1089/cmb.2017.0056. Epub 2017 May 25.


Meta-analytic framework for liquid association.

Wang L, Liu S, Ding Y, Yuan SS, Ho YY, Tseng GC.

Bioinformatics. 2017 Jul 15;33(14):2140-2147. doi: 10.1093/bioinformatics/btx138.


MetaDCN: meta-analysis framework for differential co-expression network detection with an application in breast cancer.

Zhu L, Ding Y, Chen CY, Wang L, Huo Z, Kim S, Sotiriou C, Oesterreich S, Tseng GC.

Bioinformatics. 2017 Apr 15;33(8):1121-1129. doi: 10.1093/bioinformatics/btw788.


Combined systemic elimination of MET and epidermal growth factor receptor signaling completely abolishes liver regeneration and leads to liver decompensation.

Paranjpe S, Bowen WC, Mars WM, Orr A, Haynes MM, DeFrances MC, Liu S, Tseng GC, Tsagianni A, Michalopoulos GK.

Hepatology. 2016 Nov;64(5):1711-1724. doi: 10.1002/hep.28721. Epub 2016 Oct 1.


Integrative clustering of multi-level omics data for disease subtype discovery using sequential double regularization.

Kim S, Oesterreich S, Kim S, Park Y, Tseng GC.

Biostatistics. 2017 Jan;18(1):165-179. doi: 10.1093/biostatistics/kxw039. Epub 2016 Aug 22.


Statistical Methods in Integrative Genomics.

Richardson S, Tseng GC, Sun W.

Annu Rev Stat Appl. 2016 Jun;3:181-209. Epub 2016 Apr 18.


Age-dependent increase in Kalirin-9 and Kalirin-12 transcripts in human orbitofrontal cortex.

Grubisha MJ, Lin CW, Tseng GC, Penzes P, Sibille E, Sweet RA.

Eur J Neurosci. 2016 Oct;44(7):2483-2492. doi: 10.1111/ejn.13351. Epub 2016 Aug 18.


MetaKTSP: a meta-analytic top scoring pair method for robust cross-study validation of omics prediction analysis.

Kim S, Lin CW, Tseng GC.

Bioinformatics. 2016 Jul 1;32(13):1966-73. doi: 10.1093/bioinformatics/btw115. Epub 2016 Mar 2.


Polymorphisms in α-Defensin-Encoding DEFA1A3 Associate with Urinary Tract Infection Risk in Children with Vesicoureteral Reflux.

Schwaderer AL, Wang H, Kim S, Kline JM, Liang D, Brophy PD, McHugh KM, Tseng GC, Saxena V, Barr-Beare E, Pierce KR, Shaikh N, Manak JR, Cohen DM, Becknell B, Spencer JD, Baker PB, Yu CY, Hains DS.

J Am Soc Nephrol. 2016 Oct;27(10):3175-3186. Epub 2016 Mar 3.


A computational method for genotype calling in family-based sequencing data.

Chang LC, Li B, Fang Z, Vrieze S, McGue M, Iacono WG, Tseng GC, Chen W.

BMC Bioinformatics. 2016 Jan 16;17:37. doi: 10.1186/s12859-016-0880-5.


Regionally Smoothed Meta-Analysis Methods for GWAS Datasets.

Begum F, Sharker MH, Sherman SL, Tseng GC, Feingold E.

Genet Epidemiol. 2016 Feb;40(2):154-60. doi: 10.1002/gepi.21949. Epub 2015 Dec 28.


Effects of aging on circadian patterns of gene expression in the human prefrontal cortex.

Chen CY, Logan RW, Ma T, Lewis DA, Tseng GC, Sibille E, McClung CA.

Proc Natl Acad Sci U S A. 2016 Jan 5;113(1):206-11. doi: 10.1073/pnas.1508249112. Epub 2015 Dec 22.


Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data.

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.

Nucleic Acids Res. 2016 Mar 18;44(5):e47. doi: 10.1093/nar/gkv1234. Epub 2015 Nov 17.


Integrative phenotyping framework (iPF): integrative clustering of multiple omics data identifies novel lung disease subphenotypes.

Kim S, Herazo-Maya JD, Kang DD, Juan-Guardela BM, Tedrow J, Martinez FJ, Sciurba FC, Tseng GC, Kaminski N.

BMC Genomics. 2015 Nov 11;16:924. doi: 10.1186/s12864-015-2170-4.


Genomic Copy Number Variations in the Genomes of Leukocytes Predict Prostate Cancer Clinical Outcomes.

Yu YP, Liu S, Huo Z, Martin A, Nelson JB, Tseng GC, Luo JH.

PLoS One. 2015 Aug 21;10(8):e0135982. doi: 10.1371/journal.pone.0135982. eCollection 2015.


Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition.

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.

Cancer Prev Res (Phila). 2015 Oct;8(10):1000-9. doi: 10.1158/1940-6207.CAPR-15-0178. Epub 2015 Aug 19.


The molecular landscape of premenopausal breast cancer.

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.

Breast Cancer Res. 2015 Aug 7;17:104. doi: 10.1186/s13058-015-0618-8.


Molecular and Genetic Characterization of Depression: Overlap with other Psychiatric Disorders and Aging.

Ding Y, Chang LC, Wang X, Guilloux JP, Parrish J, Oh H, French BJ, Lewis DA, Tseng GC, Sibille E.

Mol Neuropsychiatry. 2015 May;1(1):1-12.


Discovery and Classification of Fusion Transcripts in Prostate Cancer and Normal Prostate Tissue.

Luo JH, Liu S, Zuo ZH, Chen R, Tseng GC, Yu YP.

Am J Pathol. 2015 Jul;185(7):1834-45. doi: 10.1016/j.ajpath.2015.03.008. Epub 2015 May 9. Review.


Diagnostic pitfalls of discriminating lymphoma-associated effusions.

Chen HJ, Huang KY, Tseng GC, Chen LH, Bai LY, Liang SJ, Tu CY, Light RW.

Medicine (Baltimore). 2015 May;94(17):e800. doi: 10.1097/MD.0000000000000800.


Hypermethylation of BDNF and SST Genes in the Orbital Frontal Cortex of Older Individuals: A Putative Mechanism for Declining Gene Expression with Age.

McKinney BC, Lin CW, Oh H, Tseng GC, Lewis DA, Sibille E.

Neuropsychopharmacology. 2015 Oct;40(11):2604-13. doi: 10.1038/npp.2015.107. Epub 2015 Apr 16.


Involvement of cholesterol in Campylobacter jejuni cytolethal distending toxin-induced pathogenesis.

Lai CK, Su JC, Lin YH, Chang CS, Feng CL, Lin HJ, Lin CJ, Tseng GC, Liu HH, Hsieh JT, Su HL, Lai CH.

Future Microbiol. 2015;10(4):489-501. doi: 10.2217/fmb.14.119.


VSNL1 Co-Expression Networks in Aging Include Calcium Signaling, Synaptic Plasticity, and Alzheimer's Disease Pathways.

Lin CW, Chang LC, Tseng GC, Kirkwood CM, Sibille EL, Sweet RA.

Front Psychiatry. 2015 Mar 9;6:30. doi: 10.3389/fpsyt.2015.00030. eCollection 2015.


Discovering monotonic stemness marker genes from time-series stem cell microarray data.

Wang HW, Sun HJ, Chang TY, Lo HH, Cheng WC, Tseng GC, Lin CT, Chang SJ, Pal N, Chung IF.

BMC Genomics. 2015;16 Suppl 2:S2. doi: 10.1186/1471-2164-16-S2-S2. Epub 2015 Jan 21.


Imputation of Truncated p-Values For Meta-Analysis Methods and Its Genomic Application.

Tang S, Ding Y, Sibille E, Mogil J, Lariviere WR, Tseng GC.

Ann Appl Stat. 2014 Dec;8(4):2150-2174.


Missing value imputation in high-dimensional phenomic data: imputable or not, and how?

Liao SG, Lin Y, Kang DD, Chandra D, Bon J, Kaminski N, Sciurba FC, Tseng GC.

BMC Bioinformatics. 2014 Nov 5;15:346. doi: 10.1186/s12859-014-0346-6.


Novel fusion transcripts associate with progressive prostate cancer.

Yu YP, Ding Y, Chen Z, Liu S, Michalopoulos A, Chen R, Gulzar ZG, Yang B, Cieply KM, Luvison A, Ren BG, Brooks JD, Jarrard D, Nelson JB, Michalopoulos GK, Tseng GC, Luo JH.

Am J Pathol. 2014 Oct;184(10):2840-9. doi: 10.1016/j.ajpath.2014.06.025.


Bias correction for selecting the minimal-error classifier from many machine learning models.

Ding Y, Tang S, Liao SG, Jia J, Oesterreich S, Lin Y, Tseng GC.

Bioinformatics. 2014 Nov 15;30(22):3152-8. doi: 10.1093/bioinformatics/btu520. Epub 2014 Aug 1.


ADAM9 promotes lung cancer metastases to brain by a plasminogen activator-based pathway.

Lin CY, Chen HJ, Huang CC, Lai LC, Lu TP, Tseng GC, Kuo TT, Kuok QY, Hsu JL, Sung SY, Hung MC, Sher YP.

Cancer Res. 2014 Sep 15;74(18):5229-43. doi: 10.1158/0008-5472.CAN-13-2995. Epub 2014 Jul 24.


A conserved BDNF, glutamate- and GABA-enriched gene module related to human depression identified by coexpression meta-analysis and DNA variant genome-wide association studies.

Chang LC, Jamain S, Lin CW, Rujescu D, Tseng GC, Sibille E.

PLoS One. 2014 Mar 7;9(3):e90980. doi: 10.1371/journal.pone.0090980. eCollection 2014.


Meta-analysis methods for combining multiple expression profiles: comparisons, statistical characterization and an application guideline.

Chang LC, Lin HM, Sibille E, Tseng GC.

BMC Bioinformatics. 2013 Dec 21;14:368. doi: 10.1186/1471-2105-14-368.


Density features of screened lung tumors in low-dose computed tomography.

Shen WC, Liu JC, Shieh SH, Yang ST, Tseng GC, Hsu WH, Chen CY, Yu YH.

Acad Radiol. 2014 Jan;21(1):41-51. doi: 10.1016/j.acra.2013.09.021.


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