Publications

2026

• Cheng, H., Chen, Y., Ma, P., Zhong, W. Graphon Cross-Validation: Assessing Models on Network Data. International Conference on Learning Representations, 2026.
• Fang, L., Yu, X., Cai, J., Chen, Y., Wu, S., Liu, Z., Yang, Z., Lu, H., Gong, X., Liu, Y., Ma, T., Ruan, W., Abbasi, A., Zhang, J., Wang, T., Latif, E., Liu, W., Zhang, W., Kolouri, S., Zhai, X., Zhu, D., Zhong, W., Liu, T., Ma, P., Knowledge Distillation and Dataset Distillation of Large Language Models: Emerging Trends, Challenges, and Future Directions, Artificial Intelligence Review, 59, 17 (2026).
• Cheng, H., Yu, X., Wu, S., Fang, L., Cao, C., Zhang, J., Liu, T., Zhu, D., Zhong, W., Ma, P.. DCMM-Transformer: Degree-Corrected Mixed-Membership Attention for Medical Imaging. The 40th Annual AAAI Conference on Artificial Intelligence (AAAI), accepted.
• Fang, L., Wang, T., Ma, P., Zhai, X.. Generalizable and Efficient Automated Scoring with a Knowledge-Distilled Multi-Task Mixture-of-Experts. EAAI: The Symposium on Educational Advances in Artificial Intelligence, accepted.

2025

• Hu, L., Huang, T., Xie, H., Gong, X., Ren, C., Hu, Z., Yu, L., Ma, P., & Wang, D. (2025). Semi-supervised Concept Bottleneck Models. Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV), 2110–2119.

• Lu, H., Fang, L., Zeng, O., Ma, P., Zhong, W., Yuan, G.-C.. Optimal Gene Panel Selection for Targeted Spatial Transcriptomics Experiments, bioRxiv, preprint.

• Cai, J., Chen, Y., Fang, L., Zhong, W., Yuan, G.-C., Ma, P.. SpaDiff: Denoising for Sequence-based Spatial Transcriptomics via Diffusion Process, bioRxiv, preprint.

• Coshatt, S. J., Yang, H., Wu, S., Ye, J., Ma, P., Song, W.. SensorAI: A Machine Learning Framework for Sensor Data, Sensors, accepted.

• Wu, S., Feng, Y., Cheng, H., Huang, H., Li, Y., Ling, F., Ma, P., Zhong, W., Shen, Y. (2025). Personalized risk score prediction and testing policy adaptations of a COVID-19 population-based contact tracing network. Epidemiology & Infection, 153, e90.

• Xie, R., Sriram, T. N., Wu, W. B., Ma, P. (2025). Online Sequential Leveraging Sampling Method for Streaming Autoregressive Time Series with Application to Seismic Data. The Annals of Applied Statistics, accepted.

• Wang, B., Cai, J., Fang, L., Tsujikawa, M., Ma, P., & Leung, Y. F. (2025). Tensor analysis of animal behavior by matricization and feature selection. Computers in Biology and Medicine, accepted.

• Lu, H., Fang, L., Zhang, R., Li, X., Cai, J., Cheng, H., Tang, L., Liu, Z., Sun, Z., Wang, T., Zhang, Y., Zidan, A. H., Xu, J., Yu, J., Yu, M., Jiang, H., Gong, X., Luo, W., Sun, B., Chen, Y., Ma, T., Wu, S., Zhou, Y., Chen, J., Xiang, H., Zhang, J., Jahin, A., Ruan, W., Deng, K., Pan, Y., Wang, P., Li, J., Liu, Z., Zhang, L., Zhao, L., Liu, W., Zhu, D., Xing, X., Dou, F., Zhang, W., Huang, C., Liu, R., Zhang, M., Liu, Y., Sun, X., Lu, Q., Xiang, Z., Zhong, W., Liu, T., & Ma, P. (2025). Alignment and Safety in Large Language Models: Safety Mechanisms, Training Paradigms, and Emerging Challenges, arXiv:2507.19672.

• Fang, L., Meng, C., Zhao, L., Wang, T., Liu, T., Zhong, W., Ma, P. (2025). SPOT: An Active Learning Algorithm for Efficient Deep Neural Network Training. Big Data Mining and Analytics, 8(5), 1060–1074.

• Liu, Y., Yang Y., Lu, H., Cui, J., Ma, P., Zhong, W., Zhao Y. (2025). Extracting True Virus SERS Spectra from Concentration-Dependent Measurements and Data Augmentation for Virus Classification and Quantification. ACS Sensors, in press.

• Fang, L., Latif, E., Lu, H., Zhou, Y., Ma, P., and Zhai X. (2025). Efficient Multi-Task Inferencing: Model Merging with Gromov-Wasserstein Feature Alignment. The 26th International Conference on Artificial Intelligence in Education, accepted.

• Cai, J., Wu, S., Cheng, H., Zhong, W., Yuan, G., Ma, P. (2025) Protocol to boost the robustness and accuracy of spatial transcriptomics algorithms using ensemble technique, STAR Protocols.
• Lu, H., Cheng, H., Wang, Y., Xie, Y., Yan, H., Wang, X., Ma, P., Zhong, W. (2025) Mortgage Prepayment Modeling via a Smoothing Spline State Space Model, Journal of Data Science, 1-14. (Special issue in honor of Professor Xizhi Wu)
• Cheng, H., Wang, Y., Ma, P., Murdie, A. (2025) A Relational Approach to Understanding Global South Inter-Community NGO Networking, Pathways to Brokerage.

• Chen, Y., Wu, S., Zhong, W., Ma, P. (2025) Fluid Correlation: A Novel Way to Assess the Dynamic Association, Journal of Computational and Graphical Statistics.

• Ruan, W., Lyu, Y., Zhang, J., Cai, J., Shu, P., Ge, Y., Lu, Y., Gao, S., Wang, Y., Wang, P., Zhao, L., Wang, T., Liu, Y., Fang, L., Liu, Z., Li, Y., Wu, Z., Chen, J., Jiang, H., Pan, Y., Yang, Z., Chen, J., Liang, S., Zhang, W., Ma, T., Dou, Y., Zhang, J., Gong, X., Gan, Q., Zou, Y., Chen, Z., Qian, Y., Yu, S., Lu, J., Song, K., Wang, X., Sikora, A., Li, G., Li, X., Li, Q., Wang, Y., Lu, Z., Abate, Y., He, L., Zhong, W., Liu, R., Huang, C., Liu, W., Shen, Y., Ma, P., Zhu, H., Yan, Y., Zhu, D., Liu, T. (2025) Large Language Models for Bioinformatics, Quantitative Biology, 14(1), p. 70014.

2024

• Wang, T., Yang, Y., Lu, H., Cui, J., Chen, X., Ma, P., Zhong, W., Zhao, Y. (2024) Functional Regression for SERS Spectrum Transformation Across Diverse Instruments, Analyst.
• Ehsan Latif, Yifan Zhou, Shuchen Guo, Yizhu Gao, Lehong Shi, Matthew Nayaaba, Gyeonggeon Lee, Liang Zhang, Arne Bewersdorff, Luyang Fang, Xiantong Yang, Huaqin Zhao, Hanqi Jiang, Haoran Lu, Jiaxi Li, Jichao Yu, Weihang You, Zhengliang Liu, Vincent Shung Liu, Hui Wang, Zihao Wu, Jin Lu, Fei Dou, Ping Ma, Ninghao Liu, Tianming Liu, Xiaoming Zhai. (2024) A Systematic Assessment of OpenAI o1-Preview for Higher Order Thinking in Education, arXiv.
• Yu, J., Ye, Z., Ai, M., Ma, P. (2024) Optimal Subsampling for Data Streams with Measurement Constrained Categorical Responses, Journal of Computational and Graphical Statistics.
• Cai, J., Cheng, H., Wu, S., Zhong, W., Yuan, G., Ma, P. (2024) WEST: An Ensemble Method for Spatial Transcriptomics Analysis. Cell Reports Methods.
• Wu, S., Yang, B., Yang, H., Coshatt, S., Gong, X., Parasuraman, R., Conrad, J., Zhong, W., Ye, J., Ma, P., Song, W. (2024) Online Adaptively Anomaly Detection in Networked Electrical Machines by Enveloped Singular Spectrum Transformation. IEEE Internet of Things Journal, DOI: 10.1109/JIOT.2024.3476268.
• Ma, P., Chen, Y., Lu, H., Zhong, W. (2024) Bisection Grover’s Search Algorithm and Its Application in Analyzing CITE-seq Data, Journal of the American Statistical Association.
• Wang, Z., Fang, L., Cai, J., Ma, P., Zhong, W. (2024) MultiCOP: An Association Analysis of Microbiome-Metabolome Relationships, Statistics in Biosciences.
• Fang, L., Chen, Y., Zhong, W., Ma, P. (2024) Bayesian Knowledge Distillation: A Bayesian Perspective of Distillation with Uncertainty Quantification, ICML.
• Liu, Y., Chen, Y., Lu, H., Zhong, W., Yuan, G., and Ma, P. (2024) Orthogonal Multimodality Integration and Clustering in Single-cell Data, BMC Bioinformatics.
• Wang, Z., Cheng, H., Zhong, W., Ma, P., and Murdie, A. (2024) Shifting Sands: How Change-Point and Community Detection Can Enrich our Understanding of International Politics, International Interactions.
• Yang, B., Wu, S., Hu, K., Ye, J., Song, W., Ma, P., Shi, J., and Liu P. (2024), Enhanced Cyber-Attack Detection in Intelligent Motor Drives: A Transfer Learning Approach with Convolutional Neural Networks, IEEE Journal of Emerging and Selected Topics in Industrial Electronics.

2023

• Latif, E., Fang, L., Ma, P., and Zhai, X. (2023) Knowledge Distillation of LLM for Education, arXiv.
• Han, Y.,  Yu, J., Zhang, N., Meng, C.,  Ma, P., Zhong, W., and  Zou, C. (2023) Leverage classifier: another look at support vector machine, Statistica Sinica.
• Wu, S., Fang L., Zhang, J., Sriram, T. N., Coshatt, S. J., Zahiri, F., Mantooth, A., Ye, J., Zhong, W., Ma, P., Song, W. (2023) Unsupervised Anomaly Detection and Diagnosis in Power Electronic Networks: Informative Leverage and Multivariate Functional Clustering Approaches, IEEE Transactions on Smart Grid.
• Zhang, M., Chen, Y., Yu, D., Zhong, W., Zhang, J., and Ma, P. (2023) Elucidating Dynamic Cell Lineages and Gene Networks in Time-Course Single Cell Differentiation, Artificial Intelligence in the Life Sciences.
• Xie, R., Bai, S., and Ma, P. (2023) Optimal Sampling Designs for Multi-dimensional Streaming Time Series with Application to Power Grid Sensor Data, Annals of Applied Statistics, accepted.
• Wu, S., Cheng, H., Cai, J., Ma, P., and Zhong, W. (2023) Subsampling in Large Graphs Using Ricci Curvature, International Conference on Learning Representations, accepted.
• Xing, X., Shang, Z., Du, P., Ma, P., Zhong, W., and Liu J. (2023) Minimax Nonparametric Multi-sample Test under Smoothing, Statistica Sinica, accepted.

2022

• Ma, P., Chen, Y., Zhang, X., Xing, X., Ma, J., and Mahoney, M. (2022) Asymptotic analysis of sampling estimators for randomized linear algebra algorithms, Journal of Machine Learning Research.

• Zhang, J., Ma, P., Zhong, W., and Meng, C. (2022) Projection-based techniques for high-dimensional optimal transport problems, WIREs Computational Statistics, in press.

• Yu, J., Cheng, H., Zhang, J., Li, F., Zhong W., Ye, J., Song, W., and Ma, P.(2022) CONGO$^2$: Colored-node graph square model for anomaly detection and localization in smart grids, IEEE Internet of Things Journal, in press.

• Wang, Z., Dong, H., Ma, P., and Wang, Y. (2022) Estimation and model selection for nonparametric function-on-function regression, Journal of Computational and Graphical Statistics, accepted.

• Zhang, J., Meng, C., Yu, J., Zhang, M., Zhong, W., and Ma, P. (2022) An optimal transport approach for selecting a representative subsample with application in efficient kernel density estimation, Journal of Computational and Graphical Statistics.

2021

• Zhang, X., Datta,, G., Ma, P., and Zhong, W. (2021) Bayesian spline smoothing with ambiguous penalties, Canadian Journal of Statistics, in press.

• Meng. C., Yu, J., Chen, Y., Zhong, W., and Ma, P. (2021) Smoothing splines approximation using Hilbert curve basis selection, Journal of Computational and Graphical Statistics, accepted.

• Zhong, W., Ke, Y., Wang, Y., Chen, Y., Chen, J., Ma, P. (2021) Best Subset Selection: Statistical Computing Meets Quantum Computing , arXiv 2107.08359.

• Cheng, H., Yu, J., Wang, Z., Ma, P., Guo, C., Wang, B., Zhong, W., Xu, B.(2021) Details of single-molecule force spectroscopy data decoded by network-based automatic clustering algorithm, Journal of Physical Chemistry B , 125, 9660–9667. [Cover]

• Ma, J., Xu, X., Li, M., Zhang, Y., Zhang, L., Ma, P., Hou, J., Lei, Y., Liu, J., Huangfu, X., Yang, Y., Yi, X., Cheng, G., Bai, J., Zhong, X., Xu, X., Wang, Y.(2021) Predictive models of aging of the human eye based on ocular anterior segment morphology, Journal of Biomedical Informatics, 120:103855.

• Sun, S., Li, C., Chee, P.W., Paterson, A.H., Meng, C., Zhang, J., Ma, P., Robertson, J.S., Adhikari, J.(2021) High Resolution 3D Terrestrial LiDAR for Cotton Plant Main Stalk and Node Detection, Computers and Electronics in Agriculture, accepted.

• Kaushal, R., Peng, L., Singh, S. K., Zhang, M., Zhang, X., Vílchez, J. I., Wang, Z., He, D., Yang, Y., Lv, S., Xu, Z., Morcillo, R. J., Wang, W., Huang, W., Paré, P.W., Song, C., Zhu, J., Liu, R., Zhong, W., Ma, P., Zhang, H. (2021) Dicer-Like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation, Microbiome, 9:57.

• Cheng, H, Wang, Y., Ma, P., and Murdie, A. (2021) Communities and Brokers: How the Transnational Advocacy Network Simultaneously Provides Social Power and Exacerbates Global Inequalities, International Studies Quarterly, 65:724-738.

• Wang, Y., Meagher, R. B., Ambati, S., Cheng, H., Ma, P., and Phillips, B. (2021)Patients with Obstructive Sleep Apnea Have Altered Levels of Four Cytokines Associated with Cardiovascular and Kidney Disease, but Near Normal Levels with Airways Therapy , Nature and Science of Sleep , 13:457-466.

2020

• Meng, C., Yu, J., Zhang, J., Zhong, W., and Ma, P. (2020) Sufficient dimension reduction for classification using principal optimal transport direction, NeurIPS 2020 . [Code]

• Meng. C., Xie, R., Mandal, A., Zhang, X., Zhong, W., and Ma, P. (2020) LowCon: A design-based subsampling approach in a misspecified linear model, Journal of Computational and Graphical Statistics, https://doi.org/10.1080/10618600.2020.1844215.

• Phillips, B, Wang, Y., Ambati, S., Ma, P., and Meagher, R. B. (2020) Airways therapy of obstructive sleep apnea dramatically improves aberrant levels of soluble cytokines involved in autoimmune disease , Clinical Immunology, in press.

• Venkatraman P, Mills-Henry I, Padmanabhan KR, Pascuzzi P, Hassan M, Zhang J, Zhang X, Ma P, Pang CP, Dowling JE, Zhang M, Leung YF. (2020) Rods contribute to visual behaviour in larval zebrafish , Investigative Ophthalmology & Visual Science 61(12):11.

• Nychka, D., Ma, P., and Bates, D. (2020) A Conversation with Grace Wahba , Statistical Science, 35, 308–320.

• Zhang, J., Zhong, W., and Ma, P. (2020) A Review on Modern Computational Optimal Transport Methods with Applications in Biomedical Research, Modern Statistical Methods for Health Research, Springer.

• Xing, X., Liu, M., Ma, P., and Zhong, W.. (2020) Minimax nonparametric parallelism test, Journal of Machine Learning Research, 21:1−47.

• Wang, Y., Meagher, R. B., Ambati, S., Ma, P., and Phillips, B. (2020) Patients with obstructive sleep apnea have suppressed levels of soluble cytokine receptors involved in neurodegenerative disease, but normal levels with airways therapy , Sleep and Breathing, https://doi.org/10.1007/s11325-020-02205-y.

• Yao, M., Chen, W.W., Kong, J., Zhang, X., Shi, N., Zhong, S., Ma, P., Gallusci, P., Jackson, S., Liu, Y., and Hong, Y. (2020) METHYLTRANSFERASE1 and ripening modulate vivipary during tomato fruit development, Plant Physiology, DOI: https://doi.org/10.1104/pp.20.00499.

• Sun, X., Zhong, W., and Ma, P. (2021) An asymptotic and empirical smoothing parameters selection approach for smoothing spline ANOVA models in large samples , Biometrika, 108:149–166. [Code]

• Ma, P. , Zhang, X., Xing, X., Ma, J., and Mahoney, M. (2020) Asymptotic analysis of sampling estimators for randomized linear algebra algorithms , AISTATS, 1026-1035.

• Li, F., Xie, R., Wang, Z., Guo, L., Ye, J. Ma, P., Song, W.(2020) Online Distributed IoT Security Monitoring with Multidimensional Streaming Big Data , IEEE Internet of Things Journal, 7:4387-4394.

2019

• Huang, L., Yeung, W., Wang, Y., Cheng, H., Venkat, A., Li, S., Ma, P. Rasheed, K., and Kannan, K. (2020) Quantitative Structure-Mutation-Activity Relationship Tests (QSMART) Model for Protein Kinase Inhibitor Response Prediction, BMC Bioinformatics , 21,520.

• Meng, C., , Yuan, K., Zhang, J., Zhang, M., Zhong, W., and Ma, P. (2019) Large-scale optimal transport map estimation using projection pursuit, NeurIPS 2019 . [Code]

• Li, F., Xie, R., Yang, B., Guo, L., Ma, P., Shi, J., Ye, J., Song, W.(2019) Detection and identification of cyber and physical attacks on distribution power grids with PVs: an online high-dimensional data-driven approach , IEEE Journal of Emerging and Selected Topics in Power Electronics , DOI:10.1109/JESTPE.2019.2943449.

• Meng, C. , Zhang, X., Zhang, J., Zhong, W., and Ma, P. (2019) More efficient approximation of smoothing splines via space-filling basis selection , Biometrika, 107:723–735.

• Xie, R., Wang, Z., Bai, R., Zhong, W., and Ma, P.(2019) Online decentralized leverage score sampling for streaming multidimensional time series, AISTATS 2019, Proceedings of Machine Learning Research (PMLR) 89:2301-2311.

• Xie, R., Zhang, M., Venkatraman, P., Zhang, X., Zhang, G., Carmer, R., Kantola, S.A., Pang, C.P., Ma, P. Zhang, M., Zhong, W., and Leung, Y.F. (2019) Normalization of large-scale behavioural data collected from zebrafish, PLoS ONE, 14(2):e0212234.

2018

• Zhang, X., Lai, T., Zhang, P., Zhang, X., Yuan, C., Jin, Z., Li, H., Yu, Z., Qin, C., Tör, M., Ma, P., Cheng, Q., Hong, Y. (2019) Mini review: Revisiting mobile RNA silencing in plants, Plant Science 278, 113–117.

• Francis, M., Cheng, H., Ma, P., and Grider, A. (2019) Genomic Characterization of the Zinc Transcriptional Regulatory Element Reveals Potential Functional Roles of ZNF658, Biological Trace Element Research, https://doi.org/10.1007/s12011-019-1650-9.

• Zhang, X., Xie, R., and Ma, P. (2018).Statistical leveraging methods in big data, Handbook of Big Data Analytics. Springer.

• Zhang, J., Jin, H., Wang, Y., Sun, X., Ma, P., and Zhong, W. (2018). Smoothing Spline ANOVA Models and Their Applications in Complex and Massive Datasets, Topics in Splines and Applications. InTechOpen.

2017

• Sun, X., Du, P., Wang, X., and Ma, P.(2018) Optimal penalized function-on-function regression under a reproducing kernel Hilbert space framework, Journal of the American Statistical Association, 113(524): 1601–1611.

• Wang, H, Zhu, R., and Ma, P.(2018) Optimal subsampling for large sample logistic regression, Journal of the American Statistical Association,113(522): 829–844..

• Liu, Y., Ma, P., Cassidy, P. A., Carmer, R., Zhang, G., Venkatraman, P., Brown, P. A., Pang, C.P., Zhong, W., Zhang, M., and Leung, Y. F.(2017) Statistical analysis of zebrafish locomotor behaviour by generalized linear mixed models, Scientific Reports, 7, Article number: 2937.

• Akay, A., Domenico, T.D., Suen, K.M., Nabih, A., Parada, G.E., Larance, M., Medhi, R., Berkyurek, A.C., Wedeles, C.J., Zhang, X., Ma, P., Lamond, A.I., Hemberg, M., Claycomb, J.C., and Miska, E.(2017) The helicase Aquarius/EMB-4 is required to overcome intronic barriers to allow nuclear RNAi pathways to heritably silence transcription, Developmental Cell, 42, 241–255.

2016

• Ma, P., Zhang, N., Huang, J. Z. , and Zhong, W.(2017) Adaptive basis selection for exponential family smoothing splines with application in joint modeling of multiple sequencing samples, Statistica Sinica, 27, 1757-1777.

• Sun, X., Dalpiaz, D., Wu, D., Liu, J. S., Zhong, W., and Ma, P.(2016) Statistical inference for time course RNA-Seq data using a negative binomial mixed-effect model, BMC Bioinformatics, DOI: 10.1186/s12859-016-1180-9. [Software]

• Helwig, N., Shorter, K.A., Ma, P., and Hsiao-Wecksler, E.T.(2016) Smoothing spline analysis of variance models: A new tool for the analysis of cyclic biomechanical data, Journal of Biomechanics, DOI: http://dx.doi.org/10.1016/j.jbiomech.2016.07.035.

• Zhang, L., Xiang, L., Liu, Y., Venkatraman, P., Chong, L., Cho, J., Bonilla, S., Jin, Z.B., Pang, C.P., Ko, K.M., Ma, P., Zhang, M., and Leung, Y.F.(2016) A naturally-derived compound Schisandrin B enhanced light sensation in the pde6c zebrafish model of retinal degeneration, PLoS ONE, 11(3):e0149663.

2015

• Ma, P. , Mahoney, M.W, and Yu, B. (2015) A statistical perspective on algorithmic leveraging, Journal of Machine Learning Research, 16(Apr):861−911.

• Ma, P., Huang, J. Z. and Zhang, N. (2015) Efficient computation of smoothing splines via adaptive basis sampling , Biometrika, 102(3):631-645.[Supplementary Material]

• Helwig, N.E. and Ma, P.. (2016) Smoothing spline ANOVA for super-large samples: Scalable computation via rounding parameters. Statistics and Its Interface , Special Issue on Statistical and Computational Theory and Methodology for Big Data, 9:433–444.

• Helwig, N.E., Gao, Y., Wang, S., and Ma, P.. (2015)  Analyzing spatiotemporal trends in social media data via smoothing spline analysis of variance. Spatial Statistics, 14:491-504.

• Liu, Y., Carmer, R., Zhang, G., Venkatraman, P., Brown, S. A., Pang, C.P., Zhang, M., Ma, P., and Leung, Y. F. (2015) Statistical analysis of Zebrafish locomotor response , PLoS ONE, 10(10): e0139521.

• Nural, M.V., Cotterell, M.E., Peng, H., Xie, R., Ma, P., and Miller, J. (2015) Automated predictive big data analytics using ontology based semantics , International Journal of Big Data , 2(2):43-56

• Sewell, D. K., Kim, H., Ha, T. and Ma, P. (2015) A parameter estimation method for fluorescence lifetime data , BMC Research Notes, 8:230.

2014

• Ma, P. , Mahoney, M.W, and Yu, B. (2014) A statistical perspective on algorithmic leveraging, Proceedings of the 31st International Conference on Machine Learning, PMLR , 32, 91-99.

• Ma, P. and Sun, X. (2015) Leveraging for big data regression, WIREs Computational Statistics, 7:70–76.

• Kim, D.  Xiao, Z., Sun, X., Ryerson, B.,  Tkac, D., Ma, P.,  Wu, S.,  Chiang, C., X. E. Zhou, X. E.,  Xu, H. E.,  Palvimo, J.J., Chen, L, and Kemper, B. (2015) A dysregulated Acetyl/SUMO switch of FXR promotes hepatic inflammation in obesity, The EMBO Journal, 34(2), 184-199.

• Ji, L., Sasaki, T., Sun, X., Ma, P.,, Lewis, Z.A., and Schmitz, R.J. (2014) Methylated DNA is over-represented in whole-genome bisulfite sequencing data. Frontiers in Genetics, 5:341. [Data]

2013

• Zhang, L., Ma, P., Collery, R., Trowbridge, S., Zhang, M., Zhong, W., Leung, Y.F. (2014)  Expression profiling of the RPE in zebrafish smarca4 mutant revealed altered signals that potentially affect RPE and retinal differentiation. Molecular Vision. 20:56-72.

• Helwig, N.E. and Ma, P. (2015) Fast and stable multiple smoothing parameter selection in smoothing spline analysis of variance models with large samples. Journal of Computational and Graphical Statistics 24:3, 715-732.

2012

• Sun, X., Ma, P.*, Mumm, R. H.* (2012) Nonparametric method for genomics-based prediction of performance of quantitative traits involving epistasis in plant breeding , PLoS ONE 7(11): e50604.(*joint corresponding authors)

• Ma, P. (2012) A statistical journey to the centre of the Earth , Significance , 9(4):13-16.(invited feature article).

• Dalpiaz, D., He, X., and Ma, P. (2013) Bias correction in RNA-Seq short-read counts using penalized regression, Statistics in Biosciences ,5(1), 88-99. [Software]

2011

• Gu, C. and Ma, P. (2011) Nonparametric regression with cross-classified responses , Canadian Journal of Statistics,39(4), 591–609. [Software]
  • The article won the 2011 the Canadian Journal of Statistics best paper award.
• Tenorio, L, Andersson, F., de Hoop, M. and , Ma, P. (2011) Data analysis tools for uncertainty quantification of inverse problems, Inverse Problems, 27, 045001, doi:10.1088/0266-5611/27/4/045001.
  • The article was selected as a 2011 Inverse Problems Highlights article.

2010

• Lindner, D.,Song, X., Ma, P., Christensen, D. H. (2010) Inner core rotation and its variability from non-parametric modeling, Journal of Geophysical Research, 115, B04307, doi:10.1029/2009JB006294.

2009

• Ma, P., Zhong, W., and Liu, J. S. (2009)  Identifying differentially expressed genes in time course microarray data, Statistics in Biosciences, 1(2), 144-159.

• Zamdborg, L., Ma, P.(2009) Discovery of protein-DNA interactions by penalized multivariate regression, Nucleic Acids Research, 37(16), 5246-5254. [Software]

2008

• Leung, Y. F. *, Ma, P.*, Link, B. A. and Dowling, J.(2008) Factorial microarray analysis of zebrafish retinal development , Proceedings of the National Academy of Sciences, 105 (35), 12909-12914. [Microarray Data](*joint first authors)

• Ma, P. and Zhong, W.(2008) Penalized clustering of large scale functional data with multiple covariates, Journal of the American Statistical Association, 103 (482), 625-636. [Software]

• Ma, P., Zhong, W., Feng, Y., and Liu, J. S. (2008) Bayesian functional data clustering for temporal microarray data, International Journal of Plant Genomics, 2008 (2008) Article ID 231897. [Software]

2007

• Leung, Y.F. *, Ma, P.*, and Dowling, J. (2007) Gene expression profiling of zebrafish embryonic retinal pigment epithelium in vivo, Investigative Ophthalmology & Visual Science, 48(2), 881-890. [Microarray Data](*joint first authors)

• Jiang, L., Smith, J. N., Anderson, S. L., Ma, P., Mizzen, C. A., and Kelleher, N. L. (2007) Global assessment of combinatorial post-translational modification of core histones in yeast using contemporary mass spectrometry: Lys4 trimethylation correlates with degree of acetylation on the same H3 tail, Journal of Biological Chemistry, 282(38): 27923-34.

• van der Hilst, R.D., de Hoop. M.V., Wang, P., Shim,S.-H., Ma, P., Tenorio, L. (2007) Seismo-stratigraphy and thermal structure of Earth’s core-mantle boundary region, Science, 315(5820), 1813-1817. [Supplementary material]

• The article is featured in

  Science	National Geographic	EurekAlert	GeoTimes	Live Science	Live on Earth
  Fox News	Malaysia Sun	The Korea Times	The Time of India	Daily India	Zee News
  Xinhua News	Digital Silence	South Asian Women Forum	EIN News	sina.com	Netease

• Ma, P., Wang, P., Tenorio, L., de Hoop, M. V., and van der Hilst, R. D. (2007) Imaging of structure at and near the core mantle boundary using a generalized Radon transform: 2. Statistical inference of singularities, Journal of Geophysical Research , 112, B08303, doi:10.1029/2006JB004513.

2006

• Wang, P., de Hoop, M. V., van der Hilst, R. D., Ma, P., and Tenorio, L. (2006) Imaging of structure at and near the core mantle boundary using a generalized Radon transform: 1. Construction of image gathers, Journal of Geophysical Research, 111, B12304, doi:10.1029/2005JB004241.
  • The article is featured in SIAM: Society for Industrial and Applied Mathematics

• Yuan, G.C. *, Ma, P.*, Zhong, W., and Liu, J. S. (2006) Statistical assessment of the global regulatory role of histone acetylation in Saccharomyces cerevisiae, Genome Biology, 7(8):R70. [Supplementary material] (* joint first authors)

• Ma, P.*, Castillo-Davis, C.*, Zhong, W., and Liu, J. S. (2006) A data-driven clustering method for time course gene expression data, Nucleic Acids Research, 34(4), 1261-1269. [Software](* joint first authors)

2005

• Zhong, W., Zeng, P., Ma , P., Liu, J. S., and Zhu, Y. (2005) RSIR: regularized sliced inverse regression for motif discovery, Bioinformatics, 21(22), 4169-4175. [Software]

• Gu, C. and Ma, P. (2005) Optimal smoothing in nonparametric mixed-effect models, Annals of Statistics, 33(3), 1357-1379. [Software]

• Gu, C. and Ma, P. (2005) Generalized nonparametric mixed-effect models, Journal of Computational and Graphical Statistics, 14(2), 485-504. [Software]

2004

• Vio, R., Ma, P., Zhong, W., Nagy, J., Tenorio, L., and Wamsteker, W. (2004) Estimation of regularization parameters in multiple-image deblurring, Astronomy & Astrophysics, 423, 1179–1186.

Book Review

• Ma, P. (2007) Book review of Bayesian Inference for Gene Expression and Proteomics by Do, Muller and Vannucci, Briefings in Bioinformatics, 8(5):376-377; doi:10.1093/bib/bbm022.