Yang Ni

Google Scholar

Department of Statistics and Data Sciences

The University of Texas at Austin

yangni87[at]gmail[dot]com

Greetings! My name is Yang Ni (/y-ah-ng nee/). I will join the Department of Statistics, Texas A&M as a tenure-track Assistant Professor in fall 2018. I'm currently (since Jan 2016) a post-doc fellow at UT Austin working with Peter Müller. Before I joined UT, I got my PhD degree in Statistics from Rice University, supervised by Francesco Stingo and Veerabhadran Baladandayuthapani.

Areas of Interest

Methodology: Graphical models, Bayesian nonparametrics, big data computation, random networks, variable selection, clustering and feature allocation, classification.

Application: Gene/protein networks reconstruction, integrative genomics, brain connectomics, clinical trial design, tumor heterogeneity, precision medicine, biomarker detection, genetics, neuroscience, electronic health records.

Research

[14] Ni, Y., Müller, P., Diesendruck, M., Williamson, S., Zhu, Y., and Ji, Y. "Scalable Bayesian Nonparametric Clustering and Classification." Submitted.

  • Keywords: electronic health records, computation; parallel computing, clustering, classification, non-conjugate models, product partition models

[13] Ni, Y., Müller, P., Shpak M. , and Ji, Y. "Parallel-Tempered Feature Allocation for Large-scale Tumor Heterogeneity with Deep Sequencing Data." Submitted.

  • Keywords: computation, tumor heterogeneity; feature allocation, Indian buffet process, parallel tempering

[12] Ni, Y., Müller, P., Lin, W., and Ji, Y. "Bayesian Graphical Models for Computational Network Biology." BMC Bioinformatics (in press).

  • Keywords: graphical models; directed graph, undirected graph, chain graph, reciprocal graph, causality, review

[11] Ni, Y., and Müller, P. (2017), Discussion of "Sparse Graphs Using Exchangeable Random Measures." by Caron, F., and Fox, E. Journal of the Royal Statistical Society: Series B. [arxiv]

  • Keywords: random networks, graphical models, discussion

[10] Ni, Y., Stingo, F. C., Ha, M. J., Akbani, R., and Baladandayuthapani, V. "Bayesian Hierarchical Varying-sparsity Model with Application to Cancer Proteogenomics." Journal of the American Statistical Association (in press). [app]

  • Keywords: variable selection, prognostic biomarker; tumor heterogeneity, precision medicine, p-splines, thresholding prior, proteogenomics, precision medicine

[9] Shpak M., Ni, Y., Lu, J., Müller, P. "Variance in Estimated Pairwise Genetic Distance Under High versus Low Coverage Sequencing: the Contribution of Linkage Disequilibrium." Theoretical Population Biology (in press). [biorxiv]

  • Keywords: genetics; genetic distance, linkage disequilibrium, coverage, cancer genomics, pooled sampling, next-generation sequencing

[8] Ni, Y., Müller, P., Zhu, Y., and Ji, Y. "Heterogeneous Reciprocal Graphical Models." Biometrics (in press). [arxiv]

  • Keywords: Bayesian nonparametrics, graphical models; Dirichlet-multinomial allocation; model-based clustering, multiplatform genomic data, Pitman-Yor process, thresholding prior

[7] Ni, Y., Ji, Y., and Müller, P. "Reciprocal Graphical Models for Integrative Gene Regulatory Network Analysis." Bayesian Analysis (in press). [arxiv]

  • Keywords: graphical models; simultaneous equation models, Markov equivalence, directed cycles, feedback loop, multiplatform genomic data

[6] Ni, Y., Stingo, F. C., and Baladandayuthapani, V., "Bayesian Graphical Regression.'' Journal of the American Statistical Association (in press). [link] [app]

  • Keywords: graphical models; directed acyclic graph, thresholding prior, non-local prior, predictive network, subject-specific graph, varying graph structure

[5] Ni, Y., Stingo, F. C., and Baladandayuthapani, V. (2017), "Sparse Multi-dimensional Graphical Models: A Unified Bayesian Framework.'' Journal of the American Statistical Association, 112(518) 779-793 [link]

  • Keywords: graphical models; Decomposable and nondecomposable graphs, directed acyclic graphs, LDL decomposition, partially collapsed Gibbs sampler

[4] Guo, W., Ni, Y., and Ji, Y. (2015), "TEAMS: Toxicity- and Efficacy-based Dose Insertion Design with Adaptive Model Selection for Phase I/II Dose-Escalation Trials in Oncology." Statistics in Biosciences, 7(2) 432-459. [link]

  • Keywords: phase I/II clinical trial; adaptive model selection, dose insertion

[3] Ni, Y., Stingo, F.C., and Baladandayuthapani, V. (2015), "Bayesian Nonlinear Model Selection for Gene Regulatory Networks." Biometrics, 71(3) 585-595. [link]

  • Keywords: graphical models; directed acyclic graph, gene regulatory network, model and functional selection, p-splines

[2] Ni, Y., Marchetti, G. M., Baladandayuthapani, V, and Stingo, F. C. (2015), "Bayesian Approaches for Large Biological Networks.'' in Nonparametric Bayesian Methods in Biostatistics and Bioinformatics, Mitra, R. and Müller, P. (eds), Springer-Verlag. [link]

  • Keywords: graphical models, book chapter

[1] Ni, Y., Stingo, F. C., and Baladandayuthapani, V. (2014), "Integrative Bayesian Network Analysis of Genomic Data.'' Cancer Informatics, 13(s2) 39-48. [link]

  • Keywords: graphical models; data integration, glioblastoma multiforme, Bayesian network, multiplatform genomic data

Awards

[11] Travel Support, Rising Stars Symposium in Data Science, The University of Chicago, 2017

[10] Savage Award (honorable mention), Best Bayesian Dissertations, 2017

[9] Travel Support, The Third Annual Kliakhandler Conference on Bayesian Inference in Statistics and Statistical Genetics, 2017

[8] Junior Travel Support, 19th Meeting of New Researchers in Statistics and Probability, 2017

[7] Junior Travel Support, CBMS: Regional Conference on Spatial Statistics, 2017

[6] Young Researcher Award, The 10th ICSA International Conference, 2016

[5] Student Paper Award, The Section on Statistical Learning and Data Mining (SLDM) of the American Statistical Association (ASA), JSM 2016.

[4] NSF Junior Travel Support, ISBA World Meeting, Sardinia, Italy, 2016

[3] Jiann-Ping Hsu Pharmaceutical and Regulatory Sciences Award, Joint 24th ICSA Applied Statistics Symposium and 13th Graybill Conference, 2015.

[2] Young Investigator Travel Support, G70 Conference, Durham, North Carolina, 2015.

[1] Laplace Award (co-winner), top paper among the student travel award winners, The Section on Bayesian Statistical Science (SBSS) of the American Statistical Association (ASA), JSM 2014.

Thesis

Bayesian graphical models for complex biological networks (Savage award honorable mention)

Last updated: 04/2018