Publications

Notes: ^: co-first author; *: corresponding author; students underlined; [My Google Scholar Page]

Under revision:

[1] Mo C^, Ye Z^, Hatch K, Zhang Y, Wu Q, Liu S and Kochunov P, Ma T* and Chen S*. (2021+). Genetic Fine-mapping with Dense Linkage Disequilibrium Blocks: genetics of nicotine dependence. Under revision in BMC Bioinformatics. [bioRxiv Link].

[2] Belus J, Ke H, Ma T , Regenauer K, Myers B and Magidson J. (2021+). Testing Alcohol and HIV Stigmas as Mechanisms of Change in a Behavioral Treatment for Substance Use and ART Adherence for People Living with HIV in Cape Town, South Africa. Under revision in Journal of the International AIDS Society.

[3] Rose A, Belus J, Ma T , Lee J, Wan C, Reyes A, Joska J, Andersen L, Myers B and Magidson J. (2021+). An event-level analysis of the relationship between harmful alcohol use and anti-retroviral treatment non-adherence in people accessing HIV treatment in Cape Town, South Africa. Under revision in AIDS and Behavior.

[4] Gao S, Donohue B, Hatch K, Chen S, Ma T , ..., Nichols T and Kochunov P. (2021+). Comparing Empirical Kinship Derived Heritability for Imaging Genetics Traits in UK Biobank and Human Connectome Project. Under revision in NeuroImage.

[5] Kochunov P, Ma Y, Hatch K, Jahanshad N, ..., Ma T , ..., Nichols T and Hong E. (2021+). Brain-Wide vs. Genome-Wide Vulnerability Biomarkers for Severe Mental Illnesses. Under revision in Biological Psychiatry.

[6] Hanley A, Nguyen Q, Badawi D, Chen J, Ma T and Slopen N. (2021+). Timeliness in Autism Diagnosis and Intervention Among Three Birth Cohorts of Children, 2016-2018. Under revision in Pediatrics.

[7] Xing Y, Du Y, Kochunov P, Erp TV, Ma T and Calhoun V. (2021+). A novel feature selection method using multi-granularity weighted neighborhood rough set combined with entropy to identify biomarkers of mental disorders. Under revision in Expert Systems with Applications .

2021 (10):

[1] Ye Z^ , Mo C^, Liu S^, Hatch K, Gao S, Hong E, ..., Kochunov P*, Chen S* and Ma T*. (2021). White matter integrity and nicotine dependence: evaluating vertical and horizontal pleiotropy. Frontiers in Neuroscience, Accepted. [bioRxiv version]

[2] Ye Z^, Ke H^, Chen S, ..., Milton D and Ma T*. (2021). Biomarker categorization in transcriptomic meta-analysis by concordant patterns with application to Pan-cancer studies. Frontiers in Genetics, 12. [Link] [software]

[3] Saegusa T, Zhao Z, Ke H, Ye Z, Xu Z, Chen S and Ma T*. (2021). Detecting survival-associated biomarkers from heterogeneous populations. Scientific Reports , 11(1): 1-12. [pdf]

[4] Wu Q, Ma T, Liu Q, Milton D, Zhang Y and Chen S. (2021). ICN: extracting interconnected communities in gene co-expression networks. Bioinformatics. In press. (a preliminary version won the student paper award of American Statistical Association (ASA) Statistics in Imaging Section).

[5] Li Y, Rahman T, Ma T, Tang L and Tseng GC. (2021). A sparse negative binomial mixture model for clustering RNA-seq count data. Biostatistics. In press.

[6] Mo C^, Ye Z^ , Ke H^ , Lu T, Canida T , ..., Hong E, Kochunov P, Ma T* and Chen S*. (2021). A new Mendelian Randomization method to estimate causal effects of multivariate brain imaging exposures. Pacific Symposium on Biocomputing (PSB) 2022 . Accepted.

[7] Adenaiye O, Lai J, Bueno de Mesquita PJ, Hong F, ..., Ma T and Milton D. (2021). Infectious SARS-CoV-2 in Exhaled Aerosols and Efficacy of Masks During Early Mild Infection. Clinical Infectious Diseases . Accepted.

[8] Hanley A, Nguyen Q, Badawi D, Chen J, Ma T and Slopen N. (2021). The Diagnostic Odyssey of Autism: A Cross-Sectional Study of 3 Age Cohorts of Children from the 2016-2018 National Survey of Children's Health. Child and Adolescent Psychiatry and Mental Health . Accepted.

[9] Kochunov P, Ma Y, Kvarta M, ..., Ma T, Chen S, Nichols T and Hong E. (2021). Separating Clinical and Subclinical Depression by Big Data Informed Structural Vulnerability Index and Its impact on Cognition: ENIGMA Dot Product. Pacific Symposium on Biocomputing (PSB) 2022 . Accepted.

[10] Cruz-Cano R, Ma T, Yu Y, Lee M and Liu H. (2021). Forecasting COVID-19 Cases based on Social Distancing in Maryland, U.S.A.: A Time Series Approach. Disaster Medicine and Public Health Preparedness, 1-4.

2020 (6):

[1] Ma T, Ren Z and Tseng GC. (2020). Variable screening with multiple studies. Statistica Sinica , 30(2): 925–953.[pdf]

[2] Wu Q, Milton D, Xing Y, Ma T, Zhang Z and Chen S. (2020). Link Predictions for Incomplete Network Data with Outcome Misclassification. Statistics in Medicine, 40(6): 1519-1534. (a preliminary version won the student paper award at 2020 Statistical Methods in Imaging (SMI) conference).

[3] Saegusa T, Ma T, Lee MT, Li G and Chen Y. (2020). Variable selection in censored threshold regression model with applications to HIV drug adherence data. Statistics in Biosciences, 12(3): 376-398.

[4] Zeng X, Zong W, Lin C, Fang Z, Li Y, Ma T, Lewis D, Enwright J and Tseng GC. (2020). Comparative Pathway Integrator: a framework of meta-analytic integration of multiple transcriptomic studies for consensual and differential pathway analysis. Genes, 11(6): 696.

[5] Lin C, Chang L, Ma T, Oh H, ... , Tseng GC and Sibille E. (2020). Older Molecular Brain Aging in Severe Mental Illness. Molecular Psychiatry , 1-11. PMID: 32632206.

[6] Yu Y, Liu S, Tao J, Ren B, Chen Z, Li F, Nalesnik M, Ma T, ..., Tseng G and Luo J. (2020). Pten-NOLC1 fusion promotes cancers involving MET and EGFR signalings. Oncogene, 1-13. PMID: 33323972.

2019 (4):

[1] Zhu L, Huo Z, Ma T, Tseng GC. (2019). Bayesian indicator variable selection to incorporate hierarchical overlapping group structure in multi-omics applications. Annals of Applied Statistics , 13(4): 2611-2636. (a preliminary version won the ENAR distinguished student paper award).

[2] Huo Z, Zhu L, Ma T, Liu H, Han S, Liao D, Zhao J and Tseng GC. (2019). Two-way Horizontal and Vertical Omics Integration for Disease Subtype Discovery. Statistics in Biosciences , 1-22.

[3] Ma T^, Huo Z^, Kuo A^, Zhu L, ..., Song C and Tseng GC. (2019). MetaOmics - Comprehensive Analysis Pipeline and Web-based Software Suite for Transcriptomic Meta-Analysis. Bioinformatics . PMID: 30304367. [pdf] [software]

[4] Grabosch S, Bulatovic M, Zeng F, Ma T, Zhang L, Ross M, Brozick J, Fang Y, Tseng G, Kim E, Gambotto A, Elishaev E, Edwards R and Vlad, A. Cisplatin-induced immune modulation in ovarian cancer mouse models with distinct inflammation profiles. Oncogene, 38(13): 2380-2393. PMID: 30518877.

2018 (3):

[1] Fang Z, Ma T, Tang G, Zhu L, Yan Q, Wang T, Celedón JC, Chen W and Tseng GC.(2018). Bayesian integrative model for multi-omics data with missingness. Bioinformatics , 34(22): 3801-3808. PMID: 30184058.

[2] Andersen CL, Boisen MM, Sikora MJ, Ma, T., Tseng G, Suryawanshi S, Vlad AM, Elishaev E, Edwards RP and Oesterreich S. (2018). The evolution of estrogen receptor signaling in the progression of endometriosis to endometriosis-associated ovarian cancer. Hormones and Cancer, 9(6): 399-407.PMID: 30302736.

[3] Scifo E, Pabba M, Kapadia F, Ma T, Lewis DA, Tseng GC and Sibille E. (2018). Sustained molecular pathology across episodes and remission in major depressive disorder. Biological psychiatry, 83(1), pp.81-89. PMID: 28935211.

2017 (8):

[1] Ma, T. , Liang, F. and Tseng, GC. (2017). Biomarker detection and categorization in ribonucleic acid sequencing meta-analysis using Bayesian hierarchical model. Journal of the Royal Statistical Society: Series C. 66(4): 847-867. (won 2017 ASA Section on Bayesian Statistical Science (SBSS) student paper award) [pdf]

[2] Ma, T. , Liang, F., Oesterreich, S. and Tseng, GC. (2017). A joint Bayesian modeling for integrating microarray and RNA-seq transcriptomic data. Journal of Computational Biology. 24(7): 647-662. (selected to present at Dahshu Data Science Symposium: Computational Precision Health 2017 and won the best paper award) [pdf]

[3] Ma, T., Song, C. and Tseng, GC. (2017). Discussant paper on "Statistical contributions to bioinformatics: Design, modelling, structure learning and integration". Statistical Modelling , 17(4-5): 305-315. [pdf]

[4] 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 and Oesterreich S. (2017). Active estrogen receptor-alpha signaling in ovarian cancer models and clinical specimens. Clinical Cancer Research. 23(14):3802-3812. PMID: 28073843.

[5] Linkov F, Goughnoura SL, Ma T, Xu Z, Edwards RP, Lokshin AE, Ramanathan RC, Hamad GG, McCloskey C and Bovbjerg DH. (2017). Changes in inflammatory endometrial cancer-associated biomarkers in individuals undergoing surgical weight loss. Gynecologic Oncology. 147(1): 133-138.PMID: 28797697.

[6] French L, Ma T, Oh H, Tseng GC, and Sibille E. (2017). Age-related gene expression in the frontal cortex suggests synaptic function changes in specific inhibitory neuron subtypes. Frontiers in aging neuroscience , 9: 162. PMID: 28611654.

[7] Pabba M, Scifo E, Kapadia F, Nikolova YS, Ma T, Mechawar N, Tseng GC and Sibille E. (2017). Resilient protein co-expression network in male orbitofrontal cortex layer 2/3 during human aging.Neurobiology of Aging , 58: 180-190. PMID: 28750307.

[8] 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 and Birrer M. (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. PMID: 28483269 .

2016 and before (8):

[1] Liu S, Tsai W, Ding Y, Chen R, Fang Z, Huo Z, Kim S, Ma T, Chang T, Priedigkeit N, Lee AV, Luo J, Wang H, Chung I and Tseng, GC. (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(5):e47. PMID: 26582927 .

[2] Zhang L, Ma T, Brozick J, Babalola K, Budiu R, Tseng G and Vlad AM. (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. PMID: 26973247.

[3] Chen CY, Logan RW, Ma T, Lewis DA, Tseng GC, Sibille E and McClung CA. (2016). The effects of aging on circadian patterns of gene expression in the human prefrontal cortex. Proceedings of the National Academy of Sciences , 113(1), 206-21. PMID: 26699485. (High Attention Paper, 99th percentile, News on National Public Radio (NPR))

[4] Sanei-Moghaddam A, Ma T, Goughnour SL, Edwards RP, Lounder PJ, Ismail N, Comerci JT, Mansuria SM and Linkov F. (2016). Changes in hysterectomy trends after the implementation of a clinical pathway. Obstetrics & Gynecology , 127(1), 139-147. PMID: 26646126 .

[5] Mony JT, Zhang L, Ma T, Grabosch S, Tirodkar TS, Boric J, Tseng G, Elishaev E, Edwards RP, Huang X and Vlad AM. (2015). 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 Immunology, Immunotherapy 64(9):1095-108. doi: 10.1007/s00262-015-1712-6 PMID: 25998800.

[6] Liao S, Hartmaier RJ, McGuire KP, Puhalla SL, Luthra S, Chandran UR, Ma T, Bhargava R, Davidson NE, Benz S, Lee AV, Tseng GC and Oesterreich S. (2015). The molecular landscape of premenopausal breast cancer. Breast Cancer Research, 17:104. doi: 10.1186/s13058-015-0618-8. PMID: 26251034. (discussed in an interview; Nature, 527: S108-109)

[7] 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 and Vlad AM. (2014). Complement Pathway Is Frequently Altered in Endometriosis and Endometriosis-Associated Ovarian Cancer, Clinical Cancer Research, 20(23):6163-6174. doi: 10.1158/1078-0432.CCR-14-1338. PMID: 25294912.

[8] Hou L^, Ma T^ and Zhao H. (2014). Incorporating functional annotation information in prioritizing disease associated SNPs from genome wide association studies. Science China Life Sciences, 57(11): 1072-1079. PMID: 25326070.

### Books

George C. Tseng, Zhiguang Huo and Tianzhou Ma . Foundations for High-Throughput Omics Data Analysis: Methods, Theories and Applications. Chapman & Hall/CRC . In preparation and expected in 2021.