Publications and Professional Activities
Publication list (^co-first author; *corresponding/senior author; students underlined;
Also available at My Google Scholar and My Bibliography)
Software and reproducibility: For all our methodological papers, we try best to provide R packages as well as data and code (mostly in GitHub) so anyone can reproduce our result with minimal effort.
- Yujia Li, Xiangrui Zeng, Chien-wei Lin*, George C. Tseng*. (2021) Simultaneous estimation of number of clusters and feature sparsity parameter in clustering high-dimensional data. Biometrics. accepted. (R package, code and data available on GitHub)
- Peng Liu, Chien-Wei Lin, Yongseok Park*, George C. Tseng*. (2021) MethylSeqDesign: A framework for Methyl-Seq genome-wide power calculation and study design issues. Biostatistics. 22:35-50. (R package, code and data available on GitHub)
- An-Shun Tai, George Tseng, Wen-Ping Hsieh. (2021) BayICE: A Bayesian hierarchical model for semi-reference-based deconvolution of bulk transcriptomic data. Annals of Applied Statistics. 15:391-411. (R package, code and data available on GitHub)
- Chien-Wei Lin^, Lun-Ching Chang^, Tianzhou Ma, Hyunjung Oh, Beverly French, Rachel Puralewski, Fasil Mathews, Yusi Fang, David A. Lewis, James Kennedy, Daniel Mueller, Victoria Marshe, Andrew Jaffe, Qiang Chen, Gianluca Ursini, Daniel Weinberger, Anne B. Newman, Eric J. Lenze, Yuliya S. Nikolova, George C. Tseng*, Etienne Sibille*. (2021) Older Molecular Brain Age in Severe Mental Illness. Molecular Psychiatry. accepted.
- Kyle D. Ketchesin^, Wei Zong^, Mariah Hildebrand, Kelly Cahill, Madeline R. Scott, Vaish Shankar, Jill Glausier, David A. Lewis, George Tseng*, and Colleen A. McClung*. (2021) Diurnal rhythms across the human dorsal and ventral striatum. PNAS. 118(2):e2016150118.
- Mingming Gong, Peng Liu, Frank C. Sciurba, Petar Stojanov, Dacheng Tao, George C. Tseng, Kun Zhang, Kayhan Batmanghelich. (2021) Unpaired Data Empowers Association Tests. Bioinformatics. Accepted.
- Soyeon Kim, Yulong Bai, Zhenjiang Fan, Brenda Diergaarde, George C Tseng, Hyun Jung Park. (2021) The microRNA target site landscape is a novel molecular feature associating alternative polyadenylation with immune evasion activity in breast cancer. Briefings in Bioinformatics. Accepted.
- Oluwabunmi O. Olaloye^, Peng Liu^, Jessica M. Toothaker, Blake T. McCourt, Collin C. McCourt, Jenny Xiao, Erica Prochaska, Spenser Shaffer, Lael Werner, UPMC NICU Faculty, UPMC Pediatric Surgery Faculty, Jordan Gringauz, Misty Good, Jeffrey D. Goldsmith, Xiaojing An, Fujing Wang, Scott B. Snapper, Dror Shouval , Chen Kong, George Tseng, Liza Konnikova*. (2021) Single-cell analysis reveals altered innate immunity in NEC with inflammatory CD16+
CD163+ monocytes trafficking to sites of inflammation. Journal of Experimental Medicine. accepted.
- Ryan W. Logan, Xiangning Xue, Kyle D. Ketchesin, Gabriel Hoffman, Panos Roussos, George Tseng, Colleen A. McClung, and Marianne L Seney. (2021) Sex differences in molecular rhythms in the human cortex. Biological Psychiatry. accepted.
- Neil Carleton, Jian Zou, Yusi Fang, Stephen E. Koscumb, Osama Shiraz Shah, Fangyuan Chen, Sushil Beriwal, Emilia J. Diego, Adam M. Brufsky, Steffi Oesterreich, Steven D. Shapiro, Robert Ferris, Leisha A. Emens, George Tseng, Oscar C. Marroquin, Adrian V. Lee, Priscilla F. McAuliffe. (2021) Outcomes After Sentinel Lymph Node Biopsy and Radiotherapy in Older Women with Early-Stage, Estrogen Receptor–Positive Breast Cancer. JAMA Network Open. 4(4):e216322.
- Ryan W. Logan, Angela R. Ozburn, Rachel N. Arey, Kyle D. Ketchesin, Alicia Winquist, Andrew Crain, Brian T. D. Tobe, Darius Becker-Krail, Matthew B. Jarpe, Xiangning Xue, Wei Zong, Zhiguang Huo, Puja K. Parekh, Xiyu Zhu, Ethan Fitzgerald, Hui Zhang, Jeffrey Oliver-Smith, Lauren M. DePoy, Mariah Hildebrand, Evan Y. Snyder, George C. Tseng, and Colleen A. McClung. (2021) Valproate reverses mania-like behaviors in mice via preferential targeting of HDAC2. Molecular Psychiatry. accepted.
- Yao Wang, Rong Guo, Bo Chen, Tanbin Rahman, Li Cai, Yizhi Li, Yan Dong, George C. Tseng, Jidong Fang, Marianne Seney, Yanhua H. Huang. (2021) Cocaine-Induced Neural Adaptations in the Lateral Hypothalamic Melanin-Concentrating Hormone Neurons and the Role in Regulating Rapid Eye Movement Sleep After Withdrawal. Molecular Psychiatry. accepted.
- Jian-Hua Luo, Silvia Liu, Junyan Tao, Bao-Guo Ren, Katherine Luo, Zhanghui Chen, Michael Nalesnik, Kathleen Cieply, Tianzhou Ma, Shi-Yuan Cheng, Qi Chen, George Michalopoulos, Joel Nelson, Rohit Bhargava, Jun Zhang, Deqin Ma, David Jarrard, Arjun Pennathur, James Luketich, Donald DeFranco, Satdarshan P. Singh Monga, George Tseng, and Yanping Yu. (2021) Pten-NOLC1 Fusion Promotes Cancers Involving MET and EGFR Signalings. Oncogene. accepted.
- Lauren M. DePoy, Darius D. Becker-Krail, Wei Zong, Neha M. Shah, George C. Tseng, Ryan W. Logan, Colleen A. McClung. (2021) Circadian- and sex-dependent increases in intravenous cocaine self-administration in Npas2 mutant mice. Journal of Neuroscience. Accepted.
- Jessica Toothaker, Peng Liu, Rebecca Case, Collin C. McCourt, Oluwabunmi Olaloye, George Tseng, Liza Konnikova. (2021) Human Placenta Harbors a Diverse Immune Landscape With Inflammatory Potential. Developmental Cell. accepted.
- Megan M Marron, Tamara B Harris, Robert M Boudreau, Clary B Clish, Steven C Moore, Rachel A Murphy, Venkatesh L Murthy, Jason L Sanders, Ravi V Shah, George C Tseng, Stacy G Wendell, Joseph M Zmuda, Anne B Newman. (2021) A metabolite composite score attenuated a substantial portion of the higher mortality risk associated with frailty among community-dwelling older adults. J Gerontol A Biol Sci Med Sci. accepted.
- Terrell E Jones, Jian Zou, George C Tseng, Somak Roy, and Rohit Bhargava. (2021) The Utility of Next Generation Sequencing in Advanced Breast and Gynecologic Cancers: Experience of a Large Tertiary Care Women's Hospital. American Journal of Clinical Pathology. accepted.
- Zhiguang Huo, Shaowu Tang, Yongseok Park, George C. Tseng*. (2020) P-value evaluation, variability index and biomarker categorization for adaptively weighted Fisher's meta-analysis method in omics applications. Bioinformatics. 36(2):524-532. (R package at Github) (data and code)
- Zhiguang Huo*, Li Zhu, Tianzhou Ma, Song Han, Daiqing Liao, Zhao Jinying and George Tseng*. (2020) Two-way horizontal and vertical omics integration for disease subtype discovery. Statistics in Biosciences. 12:1-22. (R package, code and data available on GitHub)
- Tianzhou Ma, Zhao Ren* and George C. Tseng. (2020) Variable screening with multiple studies. Statistica Sinica. 30:925-953.
- Peng Liu^, Silvia Liu^, Yusi Fang, Xiangning Xue, Jian Zou, George Tseng*, Liza Konnikova*. (2020) Recent Advances in Computer-assisted Algorithms for Cell Subtype Identification of Cytometry Data. Frontiers in Cell and Developmental Biology. 8:234. (code and data available on GitHub)
- Yujia Li, Jessica Toothaker, Collin McCourt, Lael Werner, Scott Snapper, Dror Shouval, Omry Koran, Sameer Agnihorti, George Tseng*, Liza Konnikova*. (2020) In Utero Human Intestine Harbors Unique Metabolome Including Bacterial Metabolites. JCI Insight. 5:e138751.
- Xiangrui Zeng^, Wei Zong^, Chien-Wei Lin, Zhou Fang, Tianzhou Ma, David A. Lewis, John F. Enwright and George C. Tseng*. (2020) Comparative Pathway Integrator: a framework of meta-analytic integration of multiple transcriptomic studies for consensual and differential pathway analysis. Genes. 11:696. (R package, code and data available on GitHub)
- Martin Blohmer, Li Zhu, Jennifer Atkinson, Sushil Beriwal, Joshua Rodriguez-Lopez, Margaret Rosenzweig, Adam Brufsky, George Tseng, Peter Lucas, Adrian Lee, Steffi Oesterreich, and Rachel Jankowitz. (2020) Patient treatment and outcome after breast cancer orbital and periorbital metastases: a comprehensive case series including analysis of lobular versus ductal tumor histology. Breast Cancer Research. 22:70
- Vanessa Mitsialis, Sarah Wall, Peng Liu, Jose Ordovas-Montanes, Tamar Parmet, Michael Field, Collin McCourt, Jessica Toothaker, Jeffrey Goldsmith, Leslie Kean, George Tseng, Alex Shalek, Scott B. Snapper, and Liza Konnikova. (2020) Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn's Disease. Gastroenterology. 159:591-608.e10.
- William Paden; Kelly Barko; Rachel Puralewski; Kelly Cahill; Zhiguang Huo; Micah Shelton; George Tseng; Ryan Logan; Marianne Seney. (2019) Sex differences in adult mood and in stress-induced transcriptional coherence across mesocorticolimbic circuitry. Translational Psychiatry. 10:59.
- Megan M. Marron, Stacy G. Wendell, Robert M. Boudreau, Clary B. Clish, Adam J. Santanasto, George C. Tseng, Joseph M. Zmuda, and Anne B. Newman. (2020) Metabolites associated with walking ability among the oldest old from the CHS All Stars study. J Gerontol A Biol Sci Med Sci. 75:2371-2378.
- Lei Song, Fei Fang, Peng Liu, Gang Zeng, Hongda Liu, Yang Zhao, Xubiao Xie, George Tseng, Parmjeet Randhawa, and Kunhong Xiao. (2020) Quantitative proteomics for monitoring renal transplant injury. Proteomics - Clinical Applications. 14(4):e1900036.
- Nader Shaikh, Judith M. Martin, Alejandro Hoberman, Megan Skae, Linette Milkovich, Christi McElheny, Robert W. Hickey, Lucine V. Gabriel, Diana H. Kearney, Massoud Majd, Eglal Shalaby-Rana, George Tseng, Jay Kolls, William Horne, Zhiguang Huo, Timothy R. Shope. (2020) Biomarkers that differentiate false positive urinalyses from true urinary tract infection. Pediatric Nephrology. 35(2):321-329.
- Li Zhu, Zhiguang Huo, Tianzhou Ma, Steffi Oesterreich, George C. Tseng*. (2019) Bayesian indicator variable selection to incorporate multi-layer overlapping group structure in multi-omics applications. Annals of Applied Statistics. 13:2611-2636. (R package at Github; data and code)
- Chien-Wei Lin, Serena Liao, Peng Liu, Yongseok Park, Mei-Ling Lee, George C. Tseng*. (2019) RNASeqDesign: A framework for RNA-Seq genome-wide power calculation and study design issues. Journal of the Royal Statistical Society: Series C. 68:683-704. (R package and reproducible data/code at Github or direct download R package, data/code)
- Zhiguang Huo, Chi Song* and George C. Tseng*. (2019) Bayesian latent hierarchical model for transcriptomic meta-analysis to detect biomarkers with clustered meta-patterns of differential expression signals. Annals of Applied Statistics. 13:340-366. (data and code)
- Tianzhou Ma, Zhiguang Huo, Anche Kuo, Li Zhu, Zhou Fang, Xiangrui Zeng, Chien-Wei Lin, Silvia Liu, Lin Wang, Tanbin Rahman, Lun-Ching Chang, Sunghwan Kim, Jia Li, Yongseok Park, Chi Song, Steffi Oesterreich, Etienne Sibille and George C. Tseng*. (2019) MetaOmics: Comprehensive Analysis Pipeline and Browser-based Software Suite for Transcriptomic Meta-Analysis. Bioinformatics. 35(9):1597-1599. (R shiny software suite and packages available at Github)
- Tyler Kinzy, Timothy Starr, George Tseng and Yen-Yi Ho*. (2019) Meta-Analytic Framework for Modeling Gene Coexpression Dynamics. Statistical Applications in Genetics and Molecular Biology. 18(1).
- Marianne L. Seney, Kelly Cahill, John F. Enwright III, Ryan W. Logan, Zhiguang Huo, Wei Zong, George Tseng, and Colleen A. McClung. (2019) Novel Diurnal Rhythms in the Prefrontal Cortex in Schizophrenia Drive Differential Gene Expression. Nature Communications. 10:3355
- Li Zhu^, Jessica L. Narloch^, Sayali Onkar^, ..., George C. Tseng, ..., Steffi Oesterreich, Adrian V. Lee. (2019) Metastatic breast cancers have reduced immune cell recruitment but harbor increased macrophages relative to their matched primary tumors. Journal for ImmunoTherapy of Cancer. 7(1):265.
- Damir Vareslija, Nolan Priedigkeit, ..., Li Zhu, George C. Tseng, ..., Steffi Oesterreich, Adrian V. Lee, and Leonie S. Young. (2019) Transcriptome characterization of matched primary breast and brain metastatic tumors to detect novel actionable targets. J Natl Cancer Inst. 111(4):388-398.
- Shaikh N, Martin JM, Hoberman A, Skae M, Milkovich L, Nowalk A, McElheny C, Hickey RW, Kearney D, Majd M, Shalaby-Rana E, Tseng G, Alcorn JF, Kolls J, Kurs-Lasky M, Huo Z, Horne W, Lockhart G, Pohl H, Shope TR. (2019) Host and Bacterial Markers that Differ in Children with Cystitis and Pyelonephritis. Journal of Pediatrics. 209:146-153.
- Megan M. Marron, Tamara B. Harris, Robert M. Boudreau, Clary B. Clish, Steven C. Moore, Rachel A. Murphy, Venkatesh L. Murthy, Jason L. Sanders, Ravi V. Shah, George C. Tseng, Stacy G. Wendell, Joseph M. Zmuda, and Anne B. Newman. (2019) Metabolites associated with vigor to frailty among community-dwelling older black men. Metabolites. 9(5).
- Shannon Grabosch, Mirna Bulatovic, Feitianzhi Zeng, Tianzhou Ma, Lixin Zhang, Malcolm Ross, Joan Brozick, Yusi Fang, George Tseng, Eun Kim, Andrea Gambotto, Esther Elishaev, Robert. P Edwards and Anda M. Vlad. (2019) Cisplatin-induced immune modulation in ovarian cancer mouse models with distinct inflammation profiles. Oncogene. 38:2380-2393.
- 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. (2019) Identification of recurrent fusion genes across multiple cancer types. Scientific Reports. 9(1):1074.
- Brandon C. McKinney^, Chien-Wei Lin^, Tanbin Rahman, Hyunjung Oh, David A. Lewis, George C Tseng, Etienne Sibille. (2019) DNA Methylation in the Human Frontal Cortex Reveals a Putative Mechanism for Age-by-Disease Interactions. Translational Psychiatry. 9:39.
- Peng Liu, George Tseng, and Parmjeet Randhawa. (2019) Diagnosis of T-cell Mediated Kidney Rejection in Formalin Fixed Paraffin Embedded Tissues Using RNA-Seq Based Machine Learning Algorithms. Human Pathology. 84:283-290.
- Zhou Fang, Tianzhou Ma, Gong Tang, Li Zhu, Qi Yan, Ting Wang, Juan C. Celedon, Wei Chen* and George C. Tseng*. (2018) Bayesian integrative model for multi-omics data with missingness. Bioinformatics. 34:3801-3808. (R function, code and data available on GitHub)
- Sunghwan Kim, Dongwan Kang, Zhiguang Huo, Yongseok Park and George C. Tseng*. (2018) Meta-analytic principal component analysis in integrative omics application. Bioinformatics. 34:1321-1328. (data, code) (MetaPCA R package at lab software page)
- Kelly Cahill, Zhiguang Huo, George Tseng, Ryan Logan, Marianne Seney. (2018) Improved identification of concordant and discordant gene expression signatures using an updated rank-rank hypergeometric overlap approach. Scientific Reports. 8(1):9588. (RRHO2 R package available on GitHub)
- Nilgun Tasdemir, Emily Bossart, Zheqi Li, Zhu Li, Kevin Levine, Britta Jacobsen, George C. Tseng, Nancy E. Davidson, Steffi Oesterreich. (2018) Comprehensive 2D and 3D phenotypic characterization of human invasive lobular carcinoma cell lines. Cancer Research. 78:6209-6222
- John F. Enwright, Zhiguang Huo, Dominique Arion, John P. Corradi, George Tseng and David A. Lewis. (2018) Transcriptome alterations of prefrontal cortical parvalbumin neurons in schizophrenia. Molecular Psychiatry. 23(7):1606-1613.
- Enzo Scifo, Mohan Pabba, Fenika Kapadia, Charles Ma, David A. Lewis, George C Tseng, and Etienne Sibille. (2018) Sustained molecular pathology across episodes and remission in depression. Biological Psychiatry. 83:81-89.
- Marianne L. Seney, Zhiguang Huo, Kelly Cahill, Leon French, Rachel Puralewski, Joyce Zhang, Ryan W. Logan, George Tseng, David A. Lewis, and Etienne Sibille. (2018) Opposite molecular signatures of depression in men and women. Biological Psychiatry. 84(1):18-27.
- Tian Du, Li Zhu, Kevin M. Levine, Nilgun Tasdemir, Mathew J. Sikora, Adrian V Lee, Bennett Van Houten, George C. Tseng, Steffi Oesterreich. (2018) Invasive lobular and ductal breast carcinoma differ in immune response, protein translation efficiency and metabolism. Scientific Reports. 8(1):7205.
- Tsagianni A, Mars WM, Bhushan B, Bowen WC, Orr A, Stoops J, Paranjpe S, Tseng GC, Liu S, Michalopoulos GK. (2018) Combined systemic disruption of MET and EGFR signaling causes liver failure in normal mice. American Journal of Pathology. 188(10):2223-2235.
- Xiaojing Zheng, Catherine M. O'Connell,..., George Tseng and Toni Darville. (2018) Gene Expression Signatures Can Aid Diagnosis of Sexually Transmitted Infection-Induced Endometritis in Women. Frontiers Cellular and Infection Microbiology. 8:307.
- Courtney L. Andersen, Michelle M. Boisen, Matthew J. Sikora, Tianzhou Ma, George Tseng, Swati Suryawanshi, Anda Vlad, Esther Elishaev, Robert P Edwards, and Steffi Oesterreich. (2018) The evolution of estrogen receptor signaling in the progression of endometriosis to endometriosis-associated ovarian cancer. Hormones and Cancer. 9:399-407
- Zhiguang Huo and George C. Tseng*. (2017) Integrative Sparse K-Means With Overlapping Group Lasso in Genomic Applications for Disease Subtype Discovery. Annals of Applied Statistics. 11:1011-1039. (R package at lab software page or github) (data and code)
- Tianzhou Ma, Faming Liang and George C. Tseng*. (2017) Biomarker detection and categorization in RNA-seq meta-analysis using Bayesian hierarchical model. Journal of the Royal Statistical Society: Series C. 66:847-867. (R package at lab software page) (data/code) (this paper won 2017 ASA Section on Bayesian Statistical Science (SBSS) student paper award)
- Lin Wang^, Silvia Liu^, Ying Ding, Shin-sheng Yuan, Yen-Yi Ho, and George C. Tseng*. (2017) Meta-analytic framework for liquid association. Bioinformatics. 33:2140-2147. (data/code)
- Tianzhou Ma, Chi Song and George C. Tseng*. (2017) Discussion paper for "Statistical Contributions to Bioinformatics: Design, Modeling, Structure Learning, and Integration". Statistical Modelling. 17:305-315.
- Tianzhou Ma, Faming Liang, Steffi Oesterreich and George C. Tseng*. (2017) A joint Bayesian modeling for integrating microarray and RNA-seq transcriptomic data. Journal of Computational Biology. 24:647-662. (paper was selected to present in Dahshu Data Science Symposium: Computational Precision Health 2017) (R package at lab software page) (data and code)
- Li Zhu, Ying Ding, Cho-Yi Chen, Zhiguang Huo, Sunghwan Kim, Steffi Oesterreich and George C. Tseng*. (2017) MetaDCN: meta-analytic framework for differential coexpression network detection with an application to breast cancer. Bioinformatics. 33:1121-1129. (data and code) (software) (a preliminary version was selected to present in 2016 GLBIO/CCBC Great Lakes Bioinformatics Conference.)
- Sunghwan Kim, Steffi Oesttereich, Seyoung Kim, Yongseok Park and George C. Tseng* (2017) Integrative clustering of multi-level omics data for disease subtype discovery using sequential double regularization. Biostatistics. 18:165-179. (data & code) (software) (a preliminary version of this paper won an ENAR Distinguished Student Paper Award and an ASA Biometrics Section David P Byar Travel Award)
- Chen ZH, Yu YP, Zuo ZH, Nelson JB, Michalopoulos GK, Monga S, Liu S, Tseng G, Luo JH. (2017) Targeting genomic rearrangements in tumor cells using Cas9-mediated insertion of a suicide gene. Nature Biotechnology. 35(6):543-550
- Dominique Arion, Zhiguang Huo, John F. Enwright, John P. Corradi, George Tseng and David A. Lewis. (2017) Transcriptome alterations in prefrontal pyramidal cells distinguish schizophrenia from bipolar and major depressive disorders. Biological Psychiatry. 82:594-600.
- Leon French, TianZhou Ma, Hyunjung Oh, George C. Tseng and Etienne Sibille. (2017) Age-related gene expression in the frontal cortex suggests synaptic function changes in specific inhibitory neuron subtypes. Frontier in Aging Neuroscience. 9:162
- Dong-Mei He, Bao-Guo Ren, Silvia Liu, Lang-Zhu Tang, Kathleen Cieply, George Tseng, Yan P. Yu and Jian-Hua Luo. (2017) Oncogenic Activity of Amplified Miniature Chromosome Maintenance 8 in Human Malignancies. Oncogene. 36:3629-3639.
- Mohan Pabba, Enzo Scifo, Fenika Kapadia, Yuliya Nikolova, Charles Ma, Naguib Mechawar, George C Tseng, Etienne Sibille. (2017) Resilient protein co-expression network in cortical layer 2/3 during human aging. Neurobiology in Aging. 58:180-190.
- Zhang-Hui Chen, Yan Yu, Junyan Tao, Silvia Liu, George Tseng, Michael Nalesnik, Ronald Hamilton, Rohit Bhargava, Joel Nelson, Arjun Pennathur, Satdarshan Monga, James Luketich, George Michalopoulos, and Jianhua Luo. (2017) Expression of a MAN2A1-FER Fusion Gene by Human Liver and Other Tumor Types and Oncogenic Activity in Mice. Gastroenterology. 153:1120-1132
- Shannon Grabosch, Anda Vlad, Tianzhou Ma, Mary Strange, Joan Brozick, Brian Philips, Julia Thaller, George Tseng, Xin Huang, Kathleen Moore, Kunle Odunsi, Robert P Edwards. (2017) Multiplex Profiling Identifies Distinct Local and Systemic Alterations during Intraperitoneal Chemotherapy for Ovarian Cancer: an NRG Oncology/Gynecologic Oncology Group Study. Gynecologic Oncology. 146(1):137-145.
- Courtney L. Andersen, Matthew J. Sikora, Michelle M. Boisen, Tianzhou Ma, Alec Christie, George Tseng, Yongseok Park, Soumya Luthra, Uma Chandran, Paul Haluska, Gina Mantia-Smaldone, Kunle Odunsi, Karen McLean, Adrian V. Lee, Esther Elishaev, Robert P. Edwards, Steffi Oesterreich. (2017) Active estrogen receptor-alpha signaling in ovarian cancer models and clinical specimens. Clinical Cancer Research. 23:3802-3812
- Breno Satler Diniz, Charles F. Reynolds, Etienne Sibille, Chien-Wei Lin, George Tseng, Francis Lotrich, Howard J. Aizenstein, Meryl A. Butters. (2017) Enhanced molecular aging in late-life depression: the Senescent Associated Secretory Phenotype. American Journal of Geriatric Psychiatry. 25(1):64-72.
- Sunghwan Kim, Chien-Wei Lin and George C. Tseng*. (2016) MetaKTSP: A Meta-Analytic Top Scoring Pair Method for Robust Cross-Study Validation of Omics Prediction Analysis. Bioinformatics. 32:1966-1973. (R package at lab software page)
- Sylvia Richardson, George C. Tseng and Wei Sun (2016) Statistical Methods in Integrative Genomics. Annual Review of Statistics and Its Application. 3:181-209. (A review paper of integrative genomics for the statistical community)
- Zhiguang Huo, Ying Ding, Shuchang Liu, Steffi Oesterreich and George Tseng*. (2016) A Sparse K-means Meta-analysis framework combining multiple transcriptomic studies for disease subtype discovery. Journal of the American Statistical Association. 111:513, 27-42. (data & code) (software)
- Silvia Liu, Wei-Hsiang Tsai, Ying Ding, Rui Chen, Zhou Fang, SungHwan Kim, Tianzhou Ma, Ting-Yu Chang, Nolan Michael Priedigkeit, Adrian Lee, Jianhua Luo, Hsei-Wei Wang*, I-Fang Chung* and George C. Tseng*. (2016) Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data. Nucleic Acids Research. 44:e47.
- Chen, Cho-Yi, Logan, Ryan W., Ma, Tianzhou, Tseng, George C., Sibille, Etienne, and McClung, Colleen. (2016) The effects of aging on circadian patterns of gene expression in the human prefrontal cortex. PNAS. 113:206-11.
- Lun-Ching Chang, Bingshan Li, Zhou Fang, Scott Vrieze, Matt McGue, William G. Lacono, George C. Tseng, and Wei Chen*. (2016) A computational method for genotype calling of family-based sequencing data. BMC Bioinformatics. 17:37.
- Ferdouse Begum, Reshmi Chowdhury, Vivian G. Cheung, Stephanie Sherman, George C. Tseng, Eleanor Feingold. (2016) Regionally smoothed meta-analysis methods for GWAS datasets. Genetic Epidemiology. 40:154-60.
- Breno Satler Diniz, Etienne Sibille, Chien-Wei Lin, George Tseng, Howard J. Aizenstein, Charles F. Reynolds, Meryl A. Butters. (2016) Circulating biosignatures of late-life depression (LLD): towards a comprehensive, data-driven approach to understanding LLD pathophysiology. Journal of Psychiatric Research. 82:1-7.
- Raoul Belzeaux, Chien-Wei Lin, Ying Ding, AurÈlie Bergon, El ChÈrif Ibrahim, Gustavo Turecki, George Tseng, Etienne Sibille. (2016) Predisposition to treatment response in Major Depressive Episode: a gene coexpression-network analysis. Journal of Psychiatric Research. 81:119-26.
- Melanie J Grubisha, Chien-Wei Lin, George C Tseng, Peter Penzes, Etienne Sibille, Robert A Sweet. (2016) Age-Dependent Increase in Kalirin-9 and Kalirin-12 Transcripts in Human Orbitofrontal Cortex. European Journal of Psychiatry. 44(7):2483-2492.
- Shirish Paranjpe, William Bowen, Wendy Mars, Ann Orr, Meagan Haynes, Marie DeFrances, Silvia Liu, George Tseng, Anastasia Tsagianni, George Michalopoulos. (2016) Combined systemic elimination of MET and EGFR signaling completely abolishes liver regeneration and leads to liver decompensation. Hepatology. 64(5):1711-1724.
- Lixin Zhang, Tianzhou Ma, Joan Brozick, Kathlene Babalola, Raluca Budiu, George Tseng and Anda M. Vlad. (2016) Effects of Kras activation and Pten deletion alone or in combination on MUC1 biology and epithelial-to-mesenchymal transition in ovarian cancer. Oncogene. 35(38):5010-20.
- 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. (2016) Polymorphisms in alpha-Defensin-Encoding DEFA1A3 Associate with Urinary Tract Infection Risk in Children with Vesicoureteral Reflux. J Am Soc Nephrol. 27(10):3175-3186.
- Evan Delgado, Michelle Boisen, Robin Laskey, Rui Chen, Chi Song, Jad Sallit, Zak Yochum, Courtney L. Andersen, Matthew Sikora, Jacob Wagner, Steven Safe, Esther Elishaev, Robert P. Edwards, Paul Haluska1, George Tseng, Mark Schurdak, Steffi Oesterreich. (2016) High Expression of Orphan Nuclear Receptor NR4A1 in a Subset of Ovarian Tumors with Worse Outcome. Gynecologic Oncology. 141:348-56.
- SungHwan Kim^, Jose D. Herazo-Maya^, Dongwan D. Kang^, Brenda M. Juan-Guardela, John Tedrow, Fernando J. Martinez, F.C. Sciurba, George C. Tseng* & Naftali Kaminski*. (2015) Integrative Phenotyping Framework (iPF): Integrative Clustering of Multiple Omics Data Identifies Novel Lung Disease Subphenotypes. BMC Genomics. 16:924. (data & code) (software)
- Serena Liao, Ryan J. Hartmaier, Kandace McGuire, Shannon Puhalla, Soumya Luthra, Uma Chandran, Tianzhou Ma, Rohit Bhargava, Nancy E Davidson, Steve Benz, Adrian V. Lee*, George C. Tseng*, Steffi Oesterreich*. (2015) The molecular landscape of premenopausal breast cancer. Breast Cancer Research. 17:104. (discussed in an interview; Nature, 527: S108-109)
- Tiffany A. Katz, Serena G. Liao, Vincent J. Palmieri, Robert K. Dearth, Thushangi Pathiraja, Zhiguang Huo, Patricia Shaw, Sarah Small, Nancy E. Davidson, David G. Peters, George C. Tseng*, Steffi Oesterreich*, Adrian V. Lee*. (2015) Targeted DNA methylation screen in the mouse mammary genome reveals a parity-induced hypermethylation of IGF1R which persists long after parturition. Cancer Prevention Research. 8:1000-9.
- Ying Ding^, Lun-Ching Chang^, Xingbin Wang^, Jean-Philippe Guilloux, Jenna Parrish, Hyunjung Oh, Beverly J. French, David A. Lewis, George C. Tseng*, and Etienne Sibille*. (2015) Molecular and Genetic Characterization of Depression: Overlap with other Psychiatric Disorders and Aging. Molecular Neuropsychiatry. 1:1-12.
- Jean-Philippe Guilloux^, Sabrina Bassi^, Ying Ding^, Chris Walsh, Gustavo Turecki, George Tseng, Jill M. Cyranowski and Etienne Sibille*. (2015) Testing the predictive value of peripheral gene expression for non-remission following citalopram treatment for major depression. Neuropsychopharmacology. 40:701-10.
- Yan P. Yu^, Silvia Liu^, Zhigang Huo, Amantha Martin, Joel B. Nelson, George C. Tseng and Jian-Hua Luo. (2015) Genomic copy number variations in the genomes of leukocytes predicting prostate cancer clinical outcomes. PLOS ONE. 10:e0135982.
- Jyothi Thyagabhavan Mony, Lixin Zhang, Tianzhou Ma, Tejas Tirodkar, Shannon Grabosch, Joan Brozick, George Tseng, Esther Elishaev, Robert P. Edwards, Xin Huang and Anda M. Vlad. (2015) Anti-PD-L1 prolongs survival and triggers cytotoxic but not humoral anti-tumor immune responses in a human MUC1- expressing preclinical ovarian cancer model. Cancer Immunology, Immunotherapy. 64:1095-108.
- Brandon C. McKinne, Chien-Wei Lin, Hunjung Oh, George Tseng, David A. Lewis and Etienne Sibille. (2015) Hypermethylation of BDNF and SST Genes in the Orbital Frontal Cortex of Older Individuals: A Putative Mechanism for Declining Gene Expression with Age. Neuropsychopharmacology. 40:2604-13.
- Zuo ZH, Yu YP, Ding Y, Liu S, Martin A, Tseng G, Luo JH. (2015) Oncogenic activity of miRNA 650 in prostate cancer is mediated by suppression of CSR1 expression. American Journal of Pathology. 185:1991-9.
- Jianhua Luo, Silvia Liu, Ze-Hua Zuo, Rui Chen, George C. Tseng, Yan P. Yu. (2015) Discovery and classification of fusion transcripts in prostate cancer and normal prostate tissue. American Journal of Pathology. 185:1834-45. (a review paper for fusion gene research in prostate cancer)
- Dominique Arion, John Corradi, Shaowu Tang, Dibyadeep Datta, Franklyn Boothe, Rob Zaczek, Charles Albright, George Tseng and David A. Lewis. (2015) Distinctive transcriptome alterations of prefrontal pyramidal neurons in schizophrenia and schizoaffective disorder. Molecular Psychiatry. 20:1397-405.
- Breno S. Diniz, Etienne Sibille, Ying Ding, George Tseng, Howard Aizenstein, Francis Lotrich, , Oscar Lopez, Michael T.Lotze, William Klunk, Charles F. Reynolds III and Meryl A. Butters. (2015) Plasma Biosignature and Brain Pathology related to Persistent Cognitive Impairment in Late-Life Depression. Molecular Psychiatry. 20(5):594-601.
- Chien-wei Lin, Lun-Ching Chang, George C Tseng, Caitlin M Kirkwood, Etienne L Sibille, Robert A Sweet. (2015) VSNL1 Co-expression networks in aging include calcium signaling, synaptic plasticity, and Alzheimerís disease pathways. Frontiers in Psychiatry. 6:30.
- Hsei-Wei Wang, Hsing-Jen Sun, Ting-Yu Chang, Hung-Hao Lo, Wei-Chung Cheng, George C. Tseng, Chin-Teng Lin, Shing-Jyh Chang, Nikhil Ranjan Pal and I-Fang Chung. (2015) Discovering monotonic stemness marker genes from time-series stem cell microarray data. BMC Genomics. 16:S2.
- Shaowu Tang, Ying Ding, Etienne Sibille, Jeffrey S. Mogil, William R. Lariviere, and George C. Tseng*. (2014) Imputation of truncated p-values for meta-analysis methods and its genomic application. Annals of Applied Statistics. 8:2150-2174. (data and code)
- Chi Song and George C. Tseng*. (2014) Hypothesis setting and order statistic for robust genomic meta-analysis. Annals of Applied Statistics. 8:777-800. (software download (part of MetaDE), code and data used in the paper)
- Ying Ding^, Shaowu Tang^, Serena G. Liao, Jia Jia, Steffi Oesterreich, Yan Lin, George C. Tseng*. (2014) Bias correction for selecting the minimal-error classifier from many machine learning models. Bioinformatics. 30(22):3152-8. (data and code) (software)
- Serena G. Liao^, Yan Lin^, Dongwan D. Kang, Naftali Kaminski, Frank C. Sciurba, George C. Tseng*. (2014) Missing value imputation in high-dimensional phenomic data: Imputable or not? And how? BMC Bioinformatics. 15:346. (data and code) (software)
- Yan P. Yu^, Ying Ding^, Zhanghui Chen, Amantha Michalopoulos, Rui Chen, Zulfiqar G. Gulzar, Bing Yang, Kathleen Cieply, Alyssa Luvison, Bao-Guo Ren, James D. Brooks, David Jarrard, Joel B. Nelson, George Michalopoulos, George C. Tseng* and Jian-Hua Luo*. (2014) Novel fusion transcripts associate with progressive prostate cancer. American Journal of Pathology. 184:2840-9. (highlighted by an AJP commentary paper)
- Lun-Ching Chang, Chien-wei Lin, Stephane Jamain, George C. Tseng*, Etienne Sibille*. (2014) 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. PLOS ONE. 9(3):e90980.
- Chris Gaiteri^, Ying Ding^, Beverly French, George C. Tseng and Etienne Sibille*. (2014) Beyond Modules & Hubs: the potential of gene coexpression networks for investigating molecular mechanisms of complex brain disorders. Genes, Brain and Behavior (G2B). 13:13-24.
- Suryawanshi S, Huang X, Elishaev E, Budiu RA, Zhang L, Kim S, Donnellan N, Mantia-Smaldone G, Ma T, Tseng G, Lee T, Mansuria S, Edwards RP, Vlad AM. (2014) Complement pathway is frequently altered in endometriosis and endometriosis-associated ovarian cancer. Clinical Cancer Research. 20(23):6163-74.
- Yan P. Yu, Amantha Michalopoulos, Ying Ding, George Tseng and Jianhua Luo. (2014) High Fidelity Copy Number Analysis of Formalin-Fixed and Paraffin-Embedded Tissues Using Affymetrix Cytoscan HD Chip. PLOS ONE. 9(4): e92820.
- Lun-Ching Chang, Hui-Min Lin, Etienne Sibille, and George C. Tseng*. (2013) Meta-analysis methods for combining multiple expression profiles: comparisons, statistical characterization and an application guideline. BMC Bioinformatics. 14:368. (data and code)
- Yan P. Yu^, Ying Ding^, Rui Chen, Serena G. Liao, Bao-Guo Ren, Amantha Michalopoulos, George Michalopoulos, Joel Nelson, George C. Tseng* and Jian-Hua Luo*. (2013) Whole genome methylation sequencing reveals distinct impact of differential methylations on gene transcription in prostate cancer. American Journal of Pathology. 183:1960-70. (PMID: 24113458)
- Luo JH, Ding Y, Chen R, Michalopoulos G, Nelson J, Tseng G*, Yu YP*.(2013) Genome-wide methylation analysis of prostate tissues reveals global methylation patterns of prostate cancer. American Journal of Pathology. 182:2028-36. (PMID: 23583283, PMCID: PMC3668028)
- Marianne L. Seney, Koko Ekong, Ying Ding, George C. Tseng and Etienne Sibille1. (2013) Sex chromosome complement regulates expression of mood-related genes. Biology of Sex Differences. 4:20.
- Jose D. Herazo-Maya, Imre Noth, SungHwan Kim, Shwu Fan Ma, George C. Tseng, Brenda M. Juan-Guardela, Eleanor Feingold, Thomas J. Richards, Yves Lussier, Yong Huang, Rekha Vij, Kathleen Oare Lindell, Kevin F. Gibson, Steven D. Shapiro, Jianmin Xue, Steven R. Duncan, Joe GN Garcia and Naftali Kaminski. (2013) Peripheral blood mononuclear cell gene expression profiles predict poor outcome in idiopathic pulmonary fibrosis. Science Translational Medicine. 5:205ra136.
- Marianne Seney, Lun-Ching Chang, Hyunjung Oh, Xingbin Wang, George C. Tseng, David Lewis and Etienne Sibille1. (2013) The role of genetic sex in affect regulation and expression of GABA-related genes across species. Frontiers in Psychiatry. 4:104.
- Bon J, Liao S, Tseng GC, Sciurba FC. (2013) Considerations and pitfalls in phenotyping and reclassification of chronic obstructive pulmonary disease. Translational Research, The Journal of Laboratory and Clinical Medicine. 162:252-7.
- Yu-Chen Han, Zhong-Liang Zheng, Yan P. Yu, Rui Chen, George C. Tseng, Joel Nelson and Jian-Hua Luo. (2013) Metallothionein 1h Tumor Suppressor Activity in Prostate Cancer Is Mediated By Euchromatin Methyltransferase 1. Journal of Pathology. 230:184-193.
- George C. Tseng*, Debashis Ghosh and Eleanor Feingold. (2012) Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Research 40 (9): 3785-3799. (pdf) (PMID: 22262733, PMCID: PMC3351145)
- Ferdouse Begum, Debashis Ghosh, George C. Tseng*, Eleanor Feingold. (2012) Comprehensive literature review and statistical considerations for GWAS meta-analysis. Nucleic Acids Research 40 (9): 3777-3784. (pdf) (PMID: 22241776, PMCID: PMC3351172)
- Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng*. (2012) MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis. Nucleic Acids Research. 40(2):e15. (pdf) (software download) (PMID: 22116060, PMCID: PMC3258120)
- Xingbin Wang^, Dongwan Kang^, Kui Shen^, Chi Song, Shuya Lu, Lunching Chang, Serena G. Liao, Zhiguang Huo, Naftali Kaminski, Etienne Sibille, Yan Lin, Jia Li* and George C. Tseng*. (2012) A Suite of R Packages for Quality Control, Differentially Expressed Gene and Enriched Pathway Detection in Microarray Meta-analysis. Bioinformatics. 28:2534-2536. (ß joint first author; * joint corresponding author) (pdf) (software download)(data & code used in the paper) (PMID: 22863766)
- George C. Tseng* (2012) Book Review for "Meta-analysis and Combining Information in Genetics and Genomics". Journal of the American Statistical Association. 107:497, 435-436.
- Xingbin Wang, Yan Lin, Chi Song, Etienne Sibille* and George C Tseng*. (2012) Detecting disease-associated genes with confounding variable adjustment and the impact on genomic meta-analysis: with application to major depressive disorder. BMC Bioinformatics. 13:52. (pdf) (PMID: 22458711, PMCID: PMC3342232)
- Nalesnik MA^, Tseng GC^, Ding Y, Xiang GS, Zheng ZL, Yu Y, March JW, Michalopoulos GK, Luo JH. (2012) Gene deletions and amplifications in human hepatocellular carcinomas: correlation with hepatocyte growth regulation. American Journal of Pathology. 180: 1495-1508. (^ joint first author)
- Yu YP^, Song C^, Tseng GC, Ren BG, Laframboise W, Michalopoulos G, Nelson J and Luo JH. (2012) Genome abnormalities precede prostate cancer and predict clinical relapse. American Journal of Pathology 180:2240-2248. (^ joint first author) (news release: AJP, post-gazette, UPMC)
- Kui Shen; Shara D Rice; David A Gingrich; Dakun Wang; Zhibao Mi; Chunqiao Tian; Zhenyu Ding; Stacey L Brower; Paul R Ervin; Michael J Gabrin; George Tseng; Nan Song. (2012) Distinct genes related to drug response identified in ER positive and ER negative breast cancer cell lines by meta-analysis. PLoS ONE. 7(7):e40900.
- Jean-Philippe Guilloux, Gaelle Douillard-Guilloux, Rama Kota, Xingbin Wang, Alain Gardier, Keri Martinowich, George C. Tseng, David A. Lewis, Etienne Sibille. (2012) Molecular evidence for BDNF- and GABA-related dysfunctions in the amygdala of female subjects with Major Depression. Molecular Psychiatry. 17(11):1130-42.
- Leo A. Niemeier, Haruko Akatsu Kuffner, Chi Song, Sally E. Carty, Steven P. Hodak, Linwah Yip, Robert L. Ferris, George C. Tseng, Marina N. Nikiforova, Raja R. Seethala, Shane O. LeBeau, Michael T. Stang, Christopher Coyne, Jonas T. Johnson, Andrew F. Stewart, and Yuri E. Nikiforov. (2012) A Combined Molecular-Pathological Score to Assess Aggressive Behavior of Thyroid Papillary Microcarcinoma. Cancer. 118: 2069-2077.
- Jia Li and George C. Tseng*. (2011) An adaptively weighted statistic for detecting differential gene expression when combining multiple transcriptomic studies. Annals of Applied Statistics. 5:994-1019. (pdf) (software download)
- Sunghee Oh, Dongwan Kang, Guy N Brock and George C Tseng*. (2011) Biological impacts of missing value imputation on down-stream analyses in microarray data. Bioinformatics. 27:78-86. (PMID: 21045072; PMCID: PMC3008641)
- Rebecca D. Edmonds, Yoram Vodovotz, Claudio Lagoa, Joyeeta Dutta-Moscato, Yawching Yang, Mitchell P. Fink, Ryan M. Levy, Jose M. Prince, David J. Kaczorowski, George C. Tseng*, Timothy R. Billiar*. (2011) Transcriptomic response of murine liver to severe injury and hemorrhagic shock: a dual platform microarray analysis. Physiological Genomics. 43:1170-83. (* co-corresponding author)
- Li W, Song C, Bailey DJ, Tseng GC, Coon JJ, Wysocki VH. (2011) Statistical Analysis of Electron Transfer Dissociation Pairwise Fragmentation Patterns. Analytical Chemistry. 83(24):9540-5.
- Sunghee Oh, George C. Tseng and Etienne Sibille. (2011) Reciprocal Phylogenetic Conservation of Molecular Aging in Mouse and Human Brain. Neurobiology of Aging . 32:1331-1335. (PMID: 19729224; PMCID: PMC2888783)
- Marian Rollins-Raval, Mamatha Chivukula, George C. Tseng, Drazen Jukic, and David J. Dabbs. (2011) An Immunohistochemical Panel to Differentiate Metastatic Breast Carcinoma to Skin From Primary Sweat Gland Carcinomas With a Review of the Literature. Arch Pathol Lab Med. 135:975-983.
- Zhibao Mi, Kui Shen, Nan Song, Chunrong Cheng, Chi Song, Naftali Kaminski and George C Tseng*. (2010) Module-based prediction approach for robust inter-study prediction in microarray data. Bioinformatics. 26: 2586-2593. (PMID: 20719761; PMCID: PMC2951088)
- Kui Shen and George C Tseng*. (2010) Meta-analysis for pathway enrichment analysis when combining multiple microarray studies. Bioinformatics. 26:1316-1323. (PMID: 20410053; PMCID: PMC2865865) (software download)
- Shuya Lu, Jia Li, Chi Song, Kui Shen and George C Tseng*. (2010) Biomarker Detection in the Integration of Multiple Multi-class Genomic Studies. Bioinformatics. 26:333-340. (PMID: 19965884; PMCID: PMC2815659) (software download)
- George C. Tseng*. (2010). Visualization of multiple distributions with quantiles and Fisher information with application to tandem mass spectrometry data. Computational Statistics and Data Analysis. 54:1124-1137. (PMID: 20161641; PMCID: PMC2818137) (software download)
- Shi YK, Yu YP, Tseng GC, Luo JH. (2010) Inhibition of prostate cancer growth and metastasis using small interference RNA specific for minichromosome complex maintenance component 7. Cancer Gene Ther. 17:694-9. (PMID: 20539323)
- Gao F, Carter G, Tseng G, Chivukula M. (2010) Clinical importance of histologic grading of lobular carcinoma in situ in breast core needle biopsy specimens: current issues and controversies. Am J Clin Pathol. 133(5):767-71. (PMID: 20395524)
- Shirish Paranjpe, William C Bowen, George C. Tseng, Luo, Jian-Hua, Ann Orr and Michalopoulos, George K. (2010) RNA Interference against hepatic EGFR has suppressive effects on liver regeneration in rats. American Journal of Pathology . 176:2669-81. (PMID: 20395437; PMCID: PMC2877830)
- Olga L. Bohn, Irem Nasir, Adam Brufsky, George C Tseng, Rohit Bhargava, Kim MacManus, Mamatha Chivukula. (2010) Biomarker profile in breast carcinomas presenting with bone metastasis. Int J Clin Exp Pathol. 3:139-146. (PMID: 20126581; PMCID: PMC2809993)
- Etienne Sibille, Yingjie Wang, Jennifer Joeyen-Waldorf, Chris Gaiteri, Alexandre Surget, Sunghee Oh, Catherine Belzung, George C Tseng, and David A Lewis. (2009) A Molecular Signature of Depression in the Amygdala. American Journal of Psychiatry. 166:1011-24. (PMID: 19605536; PMCID: PMC2882057)
- Chunrong Cheng, Kui Shen, Chi Song, Jianhua Luo and George C Tseng*. (2009) Ratio Adjustment and Calibration Scheme for Gene-wise Normalization to Enhance Microarray Inter-study Prediction. Bioinformatics. 25:1655-1661. (PMID: 19414534; PMCID: PMC2732320)
- George C. Tseng, Chunrong Cheng, Yan Ping Yu, Joel Nelson, George Michalopoulos and Jian-Hua Luo. (2009) Investigating multi-cancer biomarkers and their cross-predictability in the expression profiles of multiple cancer types. Biomarker Insights. 4:57-79. (PMID: 19652763; PMCID: PMC2716681)
- Chivukula M, Bhargava R, Tseng GC and Dabbs DJ. (2009) Clinicopathologic Clinicopathologic implications of "flat epithelial atypia" in core needle biopsy specimens of the breast. American Journal of Clinical Pathology. 131:802-808. (PMID: 19461086)
- Chivukula M, Domfeh A, Carter G, Tseng GC and Dabbs DJ. (2009) Characterization of High-grade Ductal Carcinoma In Situ With and Without Regressive Changes: Diagnostic and Biologic Implications. Applied Immunohistochemistry & Molecular Morphology. 17(6):495-499. (PMID: 19407654)
- Han YC, Yu YP, Tseng GC and Luo JH. (2009) Trypsin and reduction method to prepare DNA from formalin-fixed paraffin-embedded samples for methylation analysis. Histopathology. 54:773-775. (PMID: 19438756)
- Guy N. Brock, John R. Shaffer, Richard E. Blakesley-Ball, Meredith J. Lotz, and George C. Tseng*. (2008) Which Missing Value Imputation Method to Use in Expression Profiles: a Comparative Study and Two Selection Schemes. BMC Bioinformatics. 9:12. (PMID: 18186917; PMCID: PMC2253514)
- George C. Tseng* (2008) Book Review for "Genomic Signal Processing". Biometrics. 64:10-11.
- Yan Lin, George C. Tseng, Soo Yeon Cheong, Lora J.H. Bean, Stephanie L. Sherman, Eleanor Feingold. (2008) Smarter Clustering Methods for SNP Genotype Calling. Bioinformatics. 24:2665-2671. (PMID: 18826959; PMCID: PMC2732271)
- Yu-Shuen Tsai, Chin-Teng Lin, George C. Tseng, I-Fang Chung and Nikhil Ranjan Pal. (2008) Discovery of Dominant and Dormant Genes from Expression Data Using a Novel Generalization of SNR for Multi-class Problems. BMC Bioinformatics. 9:425. (PMID: 18842155; PMCID: PMC2620271)
- Yingying Huang, George C. Tseng, Shinsheng Yuan, Ljiljana Pasa-Tolic, Mary S. Lipton, Richard D. Smith, Vicki H. Wysocki. (2008). A data mining scheme for identifying peptide structural motifs behind different MS/MS fragmentation intensity patterns. Journal of Proteome Research. 7:70-79. (PMID: 18052120; PMCID: PMC2464298)
- Hamm JT, Wilson JW, Rastogi P, Lembersky BC, Tseng GC, Song YK, Kim W, Robidoux A, Raymond JM, Kardinal CG, Shalaby IA, Ansari R, Paik S, Geyer CE, Wolmark N. (2008) Gemcitabine/Epirubicin/Paclitaxel as Neoadjuvant Chemotherapy in Locally Advanced Breast Cancer: A Phase II Trial of the NSABP Foundation Research Group. Clinical Breast Cancer. 8:257-263. (PMID: 18650156)
- Marina N. Nikiforova, George C. Tseng, David Steward, Donna Diorio, and Yuri E. Nikiforov. (2008) MicroRNA Expression Profiling of Thyroid Tumors: Biological Significance and Diagnostic Utility. Journal of Clinical Endocrinology & Metabolism 93:1600-1608. (PMID: 18270258; PMCID: PMC2386678)
- P Limaye, W Bowen, J Luo, GC Tseng, G Michalopoulos.(2008) Mechanisms of HGF and EGF mediated signaling in Transdifferentiation of Rat Hepatocytes to Biliary Epithelium. Hepatology 47:1702-1713. (PMID: 18398918; PMCID: PMC2615562)
- Alfred Guirguis, Esther Elishaev, Sung-hee Oh, George C. Tseng, Kristin Zorn, Julie A. DeLoia. (2008). Use of Gene Expression Profiles to Stage Concurrent Endometrioid Tumors for the Endometrium and Ovary. Gynecologic Oncology 108:370-376. (PMID: 18083218)
2007 and before
- George C. Tseng*. (2007). Penalized and weighted K-means for clustering with scattered objects and prior information in high-throughput biological data. Bioinformatics. 23:2247-2255. (PMID: 17597097) (Supplement Material) (software download)
- Anbupalam Thalamuthu, Indranil Mukhopadhyay, Xiaojing Zheng and George C. Tseng*. (2006) Evaluation and comparison of gene clustering methods in microarray analysis. Bioinformatics. 22:2405-2412. (PMID: 16882653)
(PDF)(simu data) (real data)
- Wei Wu, Nilesh Dave, George C. Tseng, Thomas Richards, Eric Xing, Naftali Kaminski. (2005). Comparison of normalization methods for CodeLink Bioarray data. BMC Bioinformatics. 6:309. (PMID: 16381608)
- George C. Tseng and Wing H. Wong. (2005) Tight Clustering: A Resampling-based Approach for Identifying Stable and Tight Patterns in Data. Biometrics.61:10-16. (PMID: 15737073) (PDF) (elected in August 2006 as Fast Breaking Paper in Mathematics by Essential Science Indicators) (software download)
- George C. Tseng* (2004) A comparative review of gene clustering in expression profile. Proc. 8th International Conference on Control, Automation, Robotics and Vision (ICARCV). 1320-1324.
- Xiaotong Shen, George C. Tseng, Xuegong Zhang, and Wing H. Wong. (2003) On psi-Learning. Journal of the American Statistical Association. 98:724-734. (PDF)
- George C. Tseng, Min-Kyu Oh, Lars Rohlin, James C. Liao, and Wing Hung Wong. (2001) Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Research. 29: 2549-2557. (PMID: 11410663; PMCID: PMC55725) (announced in 2003 as one of the eight most accessed papers in NAR)
- Yan Yu, Guoying Yu, George C Tseng, Kathleen Cieply, Joel Nelson, Marie Defrances, Reza Zarnegar, George Michalopoulos and Jianhua Luo. (2007). Glutathione peroxidase 3, deleted or methylated in prostate cancer, suppresses prostate cancer growth and metastasis. Cancer Research. 67:8043-50. (PMID: 17804715)
- E.Sibille, J.Su, S.Leman, A.M.Le Guisquet, Y.Ibarguen-Vargas, J.Joeyen-Waldorf, C.A. Glorioso, G.C.Tseng, M.Pezzone, R.Hen, C.Belzung. (2007) Lack of serotonin1B receptor expression leads to age-related motor dysfunction, early onset of brain molecular aging and reduced longevity. Molecular Psychiatry. 12:1042-1056. (PMID: 17420766)
- Baoguo Ren, Yan Yu, George C. Tseng, Chuanyue Wu, Ka Chen, Uma Rao, Joel Nelson, George Michalopoulos, and Jian-Hua Luo. (2007). Analysis of Integrin alpha-7 Mutations in Prostate Cancer, Liver Cancer, Glioblastoma Multiforme, and Leiomyosarcoma. JNCI. 99:868-80. (PMID: 17551147) (news release: ScienceDaily)
- C.E. Lagoa, J. Bartels, A. Barratt, G.C. Tseng , G. Clermont, M.P. Fink, T.R. Billiar, Y. Vodovotz. (2006) The role of initial trauma in the host's response to injury and hemorrhage: insights from a correlation of mathematical simulations and hepatic transcriptomic analysis. Shock. 6:592-600. (PMID: 17117135)
- Yu YP, Tseng GC, Luo JH. (2006) Inactivation of myopodin expression associated with prostate cancer relapse. Urology. 68:578-582. (PMID: 16979744)
- Jian-Hua Luo, Baoguo Ren, Sergei Keryanov, George C. Tseng, Uma N.M. Rao, Satdarshan P. Monga, Steven Strom, Anthony J. Demetris, Michael Nalesnik, Yan P. Yu, Sarangarajan Ranganathan and George K. Michalopoulos. (2006) Transcriptomic and Genomic analysis of Human Hepatocellular Carcinomas and Hepatoblastomas. Hepatology 44:1012-1024. (PMID: 17006932)
- Alejandro Sweet-Cordero, George C. Tseng, Han You, Margaret Douglass, Bing Huey, Todd Golub, Donna Albertson and Tyler Jacks. (2006) Comparison of Gene Expression and Copy Number Changes in a Murine Model of Lung Cancer. Genes, Chromosomes and Cancer. 45:338-348. (PMID: 16323170)
- Baoguo Ren, Guoying Yu, George C. Tseng, Kathleen Cieply, Tim Gavel, Joel Nelson, George Michalopoulos, Yan Ping Yu and Jian-Hua Luo. (2006) MCM7 amplification and overexpression are associated with prostate cancer progression. Oncogene. 25:1090-1098. (PMID: 16247466)
- Guoying Yu, George C. Tseng, Yan Ping Yu, Tim Gavel, Joel Nelson, Alan Wells, George Michalopoulos, Demetrius Kokkinakis, and Jian-Hua Luo. (2006) CSR1 Suppresses Tumor Growth and Metastasis of Prostate Cancer. American Journal of Pathology. 168:597-607. (PMID: 16436673)
- Yingying Huang, Joseph M. Triscari, George C. Tseng, Ljiljana Pasa-Tolic, Mary S. Lipton, Richard D. Smith, Vicki H. Wysocki. (2005) Statistical Characterization of Charge State and Residue Dependence of Low Energy CID Peptide Dissociation Patterns. Analytical Chemistry. 77:5800-5813. (PMID: 16159109)
- Juey-Jen Hwang, Paul D. Allen, George C. Tseng, Ching-Wan Lam, Lameh Fananapazir, Victor J. Dzau, and Choong-Chin Liew. (2002) Microarray gene expression profiles in dilated and hypertrophic cardiomyopathic end-stage heart failure. Physiological Genomics. 10:31-44. (PMID: 12118103)
Papers in review or in revision: (source code and data sets available for journal review)
Honors, awards and services:
- Tanbin Rahman, Hsin-En Huang, Yujia Li An-shun Tai, Wen-Ping Hsieh, George C. Tseng*. (2021) A sparse negative binomial classifier with covariate adjustment for RNA-seq data. Annals of Applied Statistics. Under revision. (R package, code and data available on GitHub)
- Yusi Fang, Chung Chang*, Yongseok Park and George C. Tseng. (2021) Heavy-tailed distribution for combining dependent p-values with asymptotic robustness. submitted.
- Tanbin Rahman^, Yujia Li^, Tianzhou Ma, Lu Tang and George C. Tseng*. (2021) A sparse negative binomial mixture model for clustering RNA-seq count data. Biostatistics. Under revision. (R package, code and data available on GitHub)
- Peng Liu, Yusi Fang, Zhao Ren, Lu Tanz, George C. Tseng*. (2021) Outcome-Guided Disease Subtyping for High-Dimensional Omics Data. Submitted. (R package, code and data available on GitHub)
- Lingsong Meng, Dorina Avram, George Tseng and Zhiguang Huo*. (2021) Outcome-guided Sparse K-means for Disease Subtype Discovery via Integrating Phenotypic Data with High-dimensional Transcriptomic Data. Under revision. Journal of the Royal Statistical Society: Series C.
- Rebecca J. Watters, Kostas Verdelis, Peter C. Lucas,Shiming Jiang, YuqingChen, Feiqi Lu, Benjamin M. Martin, GeoffreyPecar,Alejandro Restrepo-Morales,Margaret Hankins, Li Zhu, Peter Mittwede, Ryan J. Hartmaier, Peter Alexander, GeorgeC.Tseng, Kurt R. Weiss,Deborah L. Galson, Adrian V. Lee, Brendan Lee, Steffi Oesterreich. (2021) Novel, knock-in mouse model for a SNPin Steroid Receptor Co-activator-1iscorrelated with decreased bone mineral density and promotion of bone metastases.
- Fei Fang^, Peng Liu^, Yang Zhao, Rajil Mehta, George Tseng, Parmjeet Randhawa, Kunhong Xiao. (2021) Diagnosis of T-Cell-Mediated Kidney Rejection by Biopsy-Based Proteomics and Machine Learning.
- Marianne Seney, Sam-Moon Kim, Jill Glausier, Mariah Hildebrand, Xiangning Xue, Wei Zong, Jiebiao Wang, Micah Shelton, BaDoi Phan, Chaitanya Srinivasan, Andreas Pfenning, George Tseng, David Lewis, Zach Freyberg, Ryan Logan. (2021) Transcriptional alterations in opioid use disorder reveal an interplay between neuroinflammation and synaptic remodeling.
- Two polygenic mouse models for treatment-resistant major depressive disorders reveal disturbances in glutamatergic and immune systems.
- Zheqi Li, Yang Wu, Amir Bahreini, Nolan M. Priedigkeit, Kai Ding, Carol A. Sartorius, Lori Miller, Margaret Rosenzweig, George C. Tseng, Jennifer M. Atkinson, Adrian V. Lee, Steffi Oesterreich. (2021) ESR1 mutant breast cancers show elevated basal cytokeratins and immune activation.
- Zheqi Li, ..., Li Zhu, George Tseng, ..., Adrian Lee and Steffi Oesterreich. (2021) Hotspot ESR1 mutations are multimodal and contextual drivers of breast cancer metastasis.
- Jessica M Toothaker, Oluwabunmi Olaloye, Blake T McCourt, Peng Liu, Collin C McCourt, Rebecca M Case, Dean Yimlamai, Geroge Tseng, and Liza Konnikova. (2021) Human placental villi immune cells help maintain homeostasis in utero.
- Silvia Liu, Michael Nalesnik, Aatur Singhi, Michelle A. Wood-Trageser, Parmjeet Randhawa, Bao-Guo Ren, Abhinav Humar, Peng Liu, Yan-Ping Yu, George C. Tseng, George Michalopoulos and Jian-Hua Luo. (2021) Transcriptome and exome analyses of hepatocellular carcinoma reveal patterns to predict cancer recurrence in liver transplant patients.
- Sarah E. Taylor, Yusi Fang; Alyssa Wield, Susan Lang, George Tseng, Robert P. Edwards, Steffi Oesterreich, Lan Coffman. (2021) Endocrine Biomarkers in Low Grade Serous Ovarian Cancers and Serous Ovarian Tumors of Low Malignant Potential.
- Silver Medal Prize, International Mathematical Olympiad, Istanbul, Turkey, 1993.
- Fellowship for gifted students studying mathematics, Ministry of Education, Taiwan, 1993.
- UCLA Chancellor Fellowship, CA. 1999-2000.
- "Tight clustering" paper (published in Biometrics 2005) elected as a "Fast Breaking Paper" in Mathematics by Essential Science Indicators. 2006.
- Clinical Research Scholar (K12) Award, Clinical and Translational Science Institute (CTSI), NIH. 2007-2009.
- Elected for "Senior Vice Chancellor Seminar Series", University of Pittsburgh. 2010.
- Elected member, International Statistical Institute (ISI). 2012.
- President, American Statistical Association (ASA) Pittsburgh Chapter. 2015-2016.
- Statistician of the Year, American Statistical Association (ASA) Pittsburgh Chapter. 2017.
- Elected Fellow, American Statistical Association (ASA). 2017.
- Provost's Award for Excellence in Mentoring. University of Pittsburgh. 2019.
Journal editorial service:
- Methods for diagnosing prostate cancer and predicting prostate cancer relapse. (2013) Inventors: Jianhua Luo; George Michalopoulos; Joel B. Nelson; Chi Song; Chien-Cheng Tseng; Yanping Yu. US20130079241A1.
- Fusion genes associated with progressive prostate cancer. (2016) Inventors: Jianhua Luo, Yanping Yu, Joel B. Nelson, George Michalopoulos, Chien-Cheng Tseng, Ying Ding. WO2015103057.
- Methods for predicting prostate cancer relapse. (2017) Inventors: Jianhua Luo, Yanping Yu, Joel B. Nelson, George Michalopoulos, Chien-Cheng Tseng, Shuchang Liu. WO2017027473.
- Methods of treating cells containing fusion genes by genomic targeting. (2017) Inventors: Jianhua Luo, George Michalopoulos, Joel B. Nelson, , Chien-Cheng Tseng, Yanping Yu. WO2018112098.
- Transcriptome and exome analyses of hepatocellular carcinoma reveal patterns to predict cancer recurrence in liver transplant patients. (2021) Inventors: George Michalopoulos, Jianhua Luo, Michael A. Nalesnik, Aatur Dilip Singhi, Chien-Cheng Tseng, Michelle A. Wood-Trageser, Shuchang Liu, Yanping Yu. pending
- Associate editor, BMC Medical Genomics, 2010-2014.
- Associate editor, Journal of Computational and Graphical Statistics (JCGS). 2011-2012
- Editorial Board Member, Scientific Reports. 2017-2020.
- Editorial Board Member (Section Technologies and Resources for Genetics), Genes, 2018-current.
- Associate editor, Frontiers in Genetics, Statistical Genetics and Methodology. 2021-current
- Integrating omics data. (2015) Edited by George C. Tseng, Debashis Ghosh, and Xianghong Jasmine Zhou. Cambridge University Press. (Amazon link)
- SungHwan Kim, Zhiguang Huo, Yongseok Park and George C. Tseng. (2015) MetaOmics: transcriptomic meta-analysis methods for biomarker detectiion, pathway analysis and other exploratory purposes. Book chapter in Integrating omics data: statistical and computational methods.
- George C. Tseng. (2006) "Support Vector Machines" and "Classification and Regression Trees". Entries in Encyclopedia of Measurement and Statistics. Sage Publications. (Amazon)
- Cheng Li, George C. Tseng, and Wing H. Wong (2003) Model-based analysis of oligonucleotide arrays and issues in cDNA microarray analysis. Book chapter in Statistical analysis of gene expression microarray data. Edited by Terry Speed. CRC Press. 1-34. (Amazon)