Notes: ^: co-first author; *: corresponding author; students underlined;
Ke H, Ye Z, Feng L, Xu Z, Li E, and Ma T*. (2024+). NGRN: a browser-based platform for the construction, analysis and visualization of noncoding-RNA gene regulatory network from transcriptomic data. Under review.
Ke H^, Bhim A^, Pan Y, ..., Ma T* and Kochunov P*. (2024+). Predicting cerebral blood flow using voxel-wise resting-state functional MRI. Under review in Human Brain Mapping.
Feng L, Ye Z, Pan Y, ..., Chen S* and Ma T*. (2024+). Adherence to Life’s Essential 8 is associated with delayed white matter aging. Under review.
Ma T^, Yang F^, Ke H and Ren Z. (2024+). Robust Distance Correlation for Variable Screening. Under revision in Journal of Computational and Graphical Statistics. https://arxiv.org/abs/2212.13292
Chen C, Chen S, Ye Z, Shi X and Ma T. (2024+). Robust Machine Learner for Mean Estimation with Information Integration from Auxiliary Data. Under revision in Journal of the American Statistical Association.
Bankole T, Chen M, Jiang Y, ..., {\bf Ma T}, ..., Li Y. Maternal intake of soybean genistein reduced risk of high fat diet-induced obesity and non-alcoholic fatty liver disease through reshaping offspring gut microbiome, metabolome and liver transcriptome. Under review.
Kochunov P, Adhikari B, ..., Ma T, Soares J, Hong E. Functional vs. Structural Cortical Deficit Pattern Biomarkers for Major Depressive Disorder: Linked to Reduced Cerebral Blood Flow in Regionally Specific Pattern. (2024+). Under revision.
Lai J, Mesquita J, Hong F, Ma T, Cowling BJ and Milton DK. Influenza A (H3) viral aerosol shedding in nasally inoculated and naturally infected cases. (2024+). Under revision in \emph{Influenza and Other Respiratory Viruses}.
Lai J, Tai S, Ma T, Cowling BJ and Milton DK. Comparison of Viral Aerosol Shedding in Influenza, Seasonal Coronavirus, and SARS-CoV-2 in a College Community. (2024). Under revision in \emph{Clinical Infectious Diseases}.
Magidson J, Regenauer K, Johnson K, Ma T, ..., Myers B. (2024). Siyakhana: A Hybrid Type 2 Effectiveness-Implementation Stepped-Wedge Trial to Reduce Stigma Towards Substance Use and Depression Among Community Health Workers in TB/HIV Care in South Africa. Under revision.
Anvari M, Kattakuzhy S, ... Ma T, ..., Magidson J. (2024). Peer Recovery to Improve Polysubstance Use and Mobile Telemedicine Retention (PRISM): A study protocol for a randomized, hybrid type 1 effectiveness-implementation trial of peer-delivered behavioral intervention for polysubstance use and medication for opioid use disorder retention in a rural community. Under revision.
Belus J, Ke H, Ma T, Regenauer K, Myers B and Magidson J. (2024+). Effects of HIV and Alcohol Stigma on Biomarker-Confirmed Alcohol Use Following a Peer-Delivered Intervention in South Africa. Under revision in Drug and Alcohol Dependence.
Hanley A, Nguyen Q, Badawi D, Chen J, Ma T and Slopen N. (2023+). Timeliness in Autism Diagnosis and Intervention Among Three Birth Cohorts of Children, 2016-2018. Under revision in Pediatrics.
Major works
Canida T, Ke H, Chen S, Ye Z and Ma T*. (2024). Multivariate Bayesian variable selection with application to multi-trait genetic fine mapping. Journal of the Royal Statistical Society: Series C. Accepted. https://arxiv.org/abs/2212.13294 .
Wang N, Ye Z and Ma T*. (2024). TIPS: a novel pathway-guided joint model for transcriptome-wide association analysis. Briefings in Bioinformatics. Accepted.
Feng L, Ye Z, Du Z, Pan Y, Liu S, Ke H, Canida T, ..., Shenassa E* and Ma T*. (2024). Causal association
between allostatic load and accelerated white matter brain aging. American Journal of Epidemiology. Accepted. https://www.medrxiv.org/content/10.1101/2024.01.26.24301793v1
Ke H and Ma T*. (2024). NGP: a tool to detect noncoding RNA-gene regulatory pairs from expression data. Cancer Bioinformatics. In Press.
Ye Z^, Pan Y^, Mccoy R, Bi C, Chen M, Feng L,...., Ma T* and Chen S*. (2024+). Contrasting association pattern of plasma low-density lipoprotein with white matter integrity in APOE4 carriers versus non-carriers. Neurobiology of Aging. Accepted.
Feng L^, Milleson H^, Ye Z, Ke H, Canida T, ..., Ma T*. Nongenetic and genetic factors associated with white matter brain aging: exposome-wide and genome-wide association study. Genes. Special Issue: Advances in Bioinformatics and Environmental Health. Accepted.
Other works
Wu Q, Zhang Y, Ma T, Kochunov P and Chen S. (2024). A multivariate to multivariate approach for voxel-wise genome-wide association analysis. Statistics in Medicine. Accepted.
Lee H, Ma T, Ke H and Chen S. (2024). dCCA: detecting differential covariation patterns between two types of high-throughput omics data. Briefings in Bioinformatics. Accepted.
Pan Y, Hong E, Acheson A, ..., Ma T, ... Kochunov P and Chen S, A site-wise reliability analysis of the ABCD diffusion fractional anisotropy data: impact of scanner and analytical pipeline. (2024+). Human Brain Mapping. Accepted.
Pan Y, Bi C, Shardell M, Ye Z, ..., Ma T, Wang Z and Chen S. Brain-wide functional connectome analysis of 40,000 individuals reveals brain networks that show aging effects in older adults. (2024). Imaging Neuroscience. Accepted.
Pan Y, Bi C, \underline{Ye Z}, ..., {\bf Ma T}, ..., Chen S. Tobacco Smoking Functional Networks: A Whole-Brain Connectome Analysis in 24,539 Individuals. Nicotine & Tobacco Research. Accepted.
Myers B, Regenauer K, Rose A, ..., Ma T, Sibeko G and Magidson J. (2024). CHW Training to Reduce Mental Health and Substance Use Stigma and Support Re-Engagement in TB/HIV Care in South Africa: Protocol for a Randomized, Stepped Wedge Hybrid Effectiveness-Implementation Trial. Implementation Science Communications. Accepted.
Bankole T, Ma T, ..., Li Z and Li Y. The Effect of Broccoli Glucoraphanin Supplementation on Ameliorating High-Fat-Diet-2 Induced Obesity Through the Gut Microbiome and Metabolome Interface. (2024). Molecular Nutrition & Food Research. Accepted.
Donohue B, Gao S, Nichols T, ..., Ma T, ..., Hong E and Kochunov P. Accelerating heritability, genetic correlation, and genome-wide association imaging genetic analyses in big and complex pedigrees. (2024). Human Brain Mapping. Accepted.
Cruz-Cano R, Dhimal M, Thu D, Zhang L, Ma T, ..., Sapkota A. (2024). Climate Change Adaptation: Neural Network Based Early Warning System for Diarrheal Disease. Environmental Research Letters. Accepted.
Lai J, Coleman K, Tai S, ..., Ma T, Cowling BJ and Milton DK. Relative efficacy of masks and respirators as source control for viral aerosol shedding from people infected with SARS-CoV-2. (2024). eBioMedicine. Accepted.
Major works
Zong W, Rahman T, Zhu L, Zeng X, Zhang Y, Zou J, Liu S, Ren Z, Litman D, Li JJ, Osterreich S, Ma T* and Tseng GC*. (2023). Transcriptomic congruence analysis for evaluating model organisms. Proceedings of the National Academy of Sciences, 120(6). https://doi.org/10.1073/pnas.2202584120. [Story on Maryland Today] [News on Genetic Engineering and Biotechnology (GEN)] [Shiny] [R package]
Feng L^, Ye Z^, Mo C, Wang J, …, Chen S* and Ma T*. (2023). Elevated blood pressure accelerates white matter brain aging among late middle-aged women: a Mendelian Randomization study in the UK Biobank. Journal of Hypertension, 10-1097. PMID: 37682053. (a preliminary version has won the APHS/STATA SCHOLAR AWARD at APHA 2023)
Ye Z, Mo C, Liu S, Gao S, Feng L, Zhao B, Canida T, Wu Y, ..., Chen S* and Ma T*. (2023). Deciphering the causal relationship between blood pressure and white matter integrity: a Mendelian Randomization study in the UK Biobank. Journal of Neuroscience Research. Accepted.
Mo C, Wang J, Ye Z, Ke H, ..., Kochunov P, Hong E, Ma T* and Chen S*. (2023). Evaluating the causal effect of tobacco smoking on white matter brain aging: a two-sample Mendelian randomization analysis in UK Biobank. Addiction, 118(4): 739-749. 10.1111/add.16088
Mo C^, Ye Z^, Hatch K, Zhang Y, Wu Q, Liu S, Kochunov P, Ma T* and Chen S*. (2023). Genetic Fine-mapping with Dense Linkage Disequilibrium Blocks: genetics of nicotine dependence. Molecular and Cellular Neuroscience. Accepted. https://www.biorxiv.org/content/10.1101/2020.12.10.420216v1.full
Other works
Xu Z, Ma T, Tang L, Talisa VB and Chang CCH. (2023). Bayesian response adaptive randomization design with a composite endpoint of mortality and morbidity. Statistics in Medicine. Accepted. https://arxiv.org/abs/2208.08472
Zou J, Shah O, Atkinson J, Ma T, Oesterreich S, Lee A and Tseng GC. (2023). Transcriptomic congruence and selection of representative cancer models towards precision medicine. Plos Computational Biology. Accepted.
Kochunov P, Ma Y, Hatch K, ..., Ma T, Chen S and Hong E. (2023). Ancestral, Pregnancy, and Negative Early Life Risks Shape Children's Brain Dis/Similarity to Schizophrenia. Biological Psychiatry. Accepted.
Watson L, Haley D, Turpin R, Ma T, Nguyen Q, Mittel M and Dyer T. (2023) Going Beyond SAVA: Exploring Psychosocial and Structural Syndemic Effects as Predictors of HIV Risk Behaviors among Black Women. Under revision in Journal of Women's Health. Accepted.
Major works
Ke H, Ren Z, Qi, J, Chen S, Tseng G, Ye Z and Ma T*. (2022). High-dimension to high-dimension screening for detecting genome-wide epigenetic and noncoding RNA regulators of gene expression. Bioinformatics, 38(17): 4078-4087. 10.1093/bioinformatics/btac518
Ye Z^, Mo C^, Ke H^, Yan Q, …, Chen S* and Ma T*. (2022). Meta-analysis of transcriptome-wide association studies across 13 brain tissues identified novel clusters of genes associated with nicotine addiction. Genes, 13(1): 37. 10.3390/genes13010037
Other works
Xing Y, Kochunov P, Erp TV, Ma T, Calhoun V and Du Y. (2022). A novel neighborhood rough set-based feature selection method and its application to biomarker identification of schizophrenia. IEEE Journal of Biomedical and Health Informatics, 27(1), 215-226.
Kochunov P, Ma Y, Hatch K, Jahanshad N, ..., Ma T, ..., Nichols T and Hong E. (2022). Brain-Wide vs. Genome-Wide Vulnerability Biomarkers for Severe Mental Illnesses. Human Brain Mapping, 43(16): 4970-4983. 10.1002/hbm.26056
Adenaiye O, Lai J, Bueno de Mesquita PJ, Hong F, ..., Ma T and Milton D. (2022). Infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in exhaled aerosols and efficacy of masks during early mild infection. Clinical Infectious Diseases, 75(1), e241-e248. DOI: 10.1093/cid/ciab797
Major works
Ye Z^, Ke H^, Chen, S, Cruz-Cano, R, He, X, Zhang, J, Dorgan J, 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. https://doi.org/10.3389/fgene.2021.651546
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. https://doi.org/10.1038/s41598-021-82332-y
Ye Z^, Mo C^, Liu S^, Hatch K, ..., Chen S* and Ma T*. (2021). White matter integrity and nicotine dependence: evaluating vertical and horizontal pleiotropy. Frontiers in Neuroscience, 15. DOI: 10.3389/fnins.2021.738037
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, pp. 73-84.
Other works
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, 24(1), 68-84. https://doi.org/10.1093/biostatistics/kxab025
Wu Q, Ma T, Liu Q, Milton D, Zhang Y and Chen S. (2021). ICN: extracting interconnected communities in gene co-expression networks. Bioinformatics, 37(14), 1997-2003. https://doi.org/10.1093/bioinformatics/btab047. (a preliminary version won the student paper award of American Statistical Association (ASA) Statistics in Imaging Section)
Chen C, Shen B, Ma T, Wang M and Wu R. (2021). A statistical framework for recovering pseudo-dynamic networks from static data. Bioinformatics, 38(9): 2481-2487. https://doi.org/10.1093/bioinformatics/btac038
Rose A, Belus J, Ma T, Lee J, Wan C, Reyes A, Joska J, Andersen L, Myers B and Magidson J. (2021). The Relationship Between Harmful Alcohol Use and Antiretroviral Non-adherence in People Accessing HIV Treatment in Cape Town, South Africa: An Event-Level Analysis. AIDS and Behavior, 26(6): 2055-2066. DOI: 10.1007/s10461-021-03552-x
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. NeuroImage, 245:118700. DOI: 10.1016/j.neuroimage.2021.118700
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, pp. 133-143.
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, 15(1), 1-9. DOI: 10.1186/s13034-021-00409-y
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. DOI: 10.1017/dmp.2021.153
Major works
Ma T, Ren Z and Tseng GC. (2020). Variable screening with multiple studies. Statistica Sinica, 30(2): 925-953.
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.
Other works
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. https://doi.org/10.1002/sim.8856
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. https://doi.org/10.3390/genes11060696
Lin C, Chang L, Ma T, Oh H, French, B, ..., Tseng G and Sibille E. (2020). Older Molecular Brain Aging in Severe Mental Illness. Molecular Psychiatry, 1-11. DOI: 10.1038/s41380-020-0834-1
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, 40 (6), 1064-1076. DOI: 10.1038/s41388-020-01582-8
Major works
Ma T^, Huo Z^, Kuo A^, ..., Song C and Tseng GC. (2019). MetaOmics - Comprehensive Analysis Pipeline and Web-based Software Suite for Transcriptomic Meta-Analysis. Bioinformatics, 35(9): 1597-1599. 10.1093/bioinformatics/bty825
Other works
Zhu L, Huo Z, Ma T and Tseng G. (2019). Bayesian indicator variable selection model with multi-layer overlapping groups. Annals of Applied Statistics, 13(4): 2611-2636. DOI: 10.1214/19-AOAS1271. (a preliminary version won the ENAR 2018 distinguished student paper award).
Huo Z, Zhu L, Ma T, ..., Zhao J and Tseng G. (2019). Two-way Horizontal and Vertical Omics Integration for Disease Subtype Discovery. Statistics in Biosciences, 12(1): 1-22. https://doi.org/10.1007/s12561-019-09242-6
Grabosch S, Bulatovic M, Zeng F, Ma T, ..., Edwards R and Vlad A. (2019). Cisplatin-induced immune modulation in ovarian cancer mouse models with distinct inflammation profiles. Oncogene, 38(13): 2380-2393. DOI: 10.1038/s41388-018-0581-9
Fang Z, Ma T, Zhu L, ..., Tang G and Tseng GC. (2018). Bayesian integrative model for multi-omics data with missingness. Bioinformatics, 34(22):3801-3808. https://doi.org/10.1093/bioinformatics/bty775
Andersen CL, Boisen MM, Sikora MJ, Ma T, ..., 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. DOI: 10.1007/s12672-018-0350-9
Scifo E, Pabba M, Kapadia F, Ma T, Lewis DA, Tseng GC and Sibille E. (2018). Sustained molecular pathology across episodes and remission in depression. Biological Psychiatry, 83(1): 81-89.
Ma T, Liang F and Tseng GC. (2017). Biomarker detection and categorization in ribonucleic acid sequencing meta-analysis using Bayesian hierarchical models. Journal of the Royal Statistical Society: Series C, 66(4): 847-867. doi: 10.1111/rssc.12199. (won ASA Section on Bayesian Statistical Science (SBSS) student paper award to attend 2017 JSM, reported on RNA-Seq Blog)
Ma T, Liang F, Oesterreich S and Tseng GC. (2017). A Joint Bayesian Model for Integrating Microarray and RNA Sequencing Transcriptomic Data. Journal of Computational Biology, 24(7): 647-662. doi: 10.1089/cmb.2017.0056. (selected to present at Dahshu Data Science Symposium: Computational Precision Health 2017 and won the best paper award)
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. https://doi.org/10.1177/1471082X1770599
Andersen CL, Sikora MJ, Boisen MM, Ma T, ..., 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.
Linkov F, Goughnoura SL, Ma T, Xu Z, ..., McCloskey C and Bovbjerg DH. (2017). Changes in inflammatory endometrial cancer-associated biomarkers in individuals undergoing surgical weight loss. Gynecologic Oncology, 147(1):133-8. DOI: 10.1016/j.ygyno.2017.07.144
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. DOI: 10.3389/fnagi.2017.00162
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. DOI: 10.1016/j.neurobiolaging.2017.06.023
Liu S, Tsai W, Ding Y, Chen R, Fang Z, Huo Z, Kim S, Ma T, ..., 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.
Zhang L, Ma T, ..., 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. DOI: 10.1038/onc.2016.53
Chen CY, Logan RW, Ma T, Lewis DA, Tseng GC, Sibille E and McClung CA. (2016). 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. DOI: 10.1073/pnas.1508249112. (High Attention Paper, 99th percentile, News on National Public Radio (NPR)).
Sanei-Moghaddam A, Ma T, ..., Mansuria SM and Linkov F. (2016). Changes in hysterectomy trends after the implementation of a clinical pathway. Obstetrics & Gynecology, 127(1), 139-147. DOI: 10.1097/AOG.0000000000001185
Mony JT, Zhang L, Ma T, ..., 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
Liao S, Hartmaier RJ, McGuire KP, Puhalla SL, Luthra S, Chandran UR, Ma T, ..., Tseng GC and Oesterreich S. (2015). The molecular landscape of premenopausal breast cancer. Breast Cancer Research, 17(1): 1-13. DOI: 10.1186/s13058-015-0618-8. (discussed in an interview; Nature, 527: S108-109)
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. DOI: 10.1007/s11427-014-4754-7
Suryawanshi S, Huang X, Elishaev E, Budiu RA, Zhang L, Kim S, Donnellan N, Mantia-Smaldone G, Ma T, ..., 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