Dalhousie University

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Current Students and postdoc:

Shuangming Yang, PhD candidate. (2022/9-) Co-supervised with Toby Kenney. Dynamic modelling for omics data.

Sarah Jennifer Organ, PhD candidate. (2022/9-) Co-supervised with Joseph Bielawski (Biology) and Amina Stoddart (Centre for Water Resources Studies). Integrative analysis of waste water microbiome data for monitoring of wastewater treatment processes.

Fatemeh Tofighi Khelejan. PhD candidate. (2021/9-). Co-supervised with Kenney (Math. and Stat. Dept., Dalhousie). Model adequacy tests and sensitivity analysis for amino acid substitution models and codon models.

Shanglun Li, PhD candidate. (2021/1-). Co-supervised with Kenney (Math. and Stat. Dept., Dalhousie). State Space OU process Models for Microbial Time Series Data.

Paul Bjorndahl, PhD candidate. (2020/1-) Co-supervised with Joseph Bielawski. (Biology Dept. in Dalhousie). Modelling the dynamics of subcommunities of ocean lake microbiome.

Xinyue Zhang, PhD candidate. (2019/1-). Co-supervised with Kenney (Math. and Stat. Dept., Dalhousie). Combining deep learning neural networks and spatiotemporal models for prediction and inference of residential house prices for property assessment.

Lihui Liu, PhD candidate. (2014/1-). Co-supervised with Kenney. Biomarker selection and predictive models for microbiome data.

Yurunyun Wang. MSc candidate. (2021/9-). Co-supervised with Kenney (Math. and Stat. Dept., Dalhousie). Medical image analysis to assist diagnoses using X-ray images.

Graduated Ph.D. Students:

Chaoyue Liu (2016/5-2022/09). Co-supervised with Robert Beiko (Computer Science). Inference of Gene Coevolution Based on Phylogenetic Profiles.

Yun Cai (2014/9-2022/08). Co-supervised with Toby Kenney. Measurement Error Deconvolution Methods and Rank Selection for Non-Negative Matrix Factorization with Applications in Microbiome Data.

Shen (Lisa) Ling. (2014/09-2022/08). Co-supervised with Toby Kenney. A New Method for Multi-Class Classification with Multiple Data Sources, with Application to Abdominal Pain Diagnosis.

Melanie Abeysundera. (2007-2011). Co-supervised with Chris Field. Phylogenetic analysis of multiple genes based on spectral methods. Employed by Statistics Canada.

Xiaofei Shi, Ph.D. (2001-2006). Co-supervised with Chris Field. Phylogenetic inferences and pattern classification. Senior analyst at CitiBank, Toronto.


Graduated M.Sc. Students:

Mia Parenteau, MSc candidate. (2018/9-2020/12). Violence detection in crowd footage: statistical features using transformed optical flow.

Wanru Jia, MSc candidate. (2018/9-2020/12). Co-supervised with Toby Kenney. Edge Detection Operators for X-ray Images Based on Hessian Matrices.

Mary Molly Hayes, MSc (2017/9-2020/5) Co-supervised with Morgan Langille (Pharmacology, Dalhousie University). Cross-Study Analyses of Microbial Abundance Using Generalized Common Factor Methods.

Paul Bjorndahl, MSc (2017/9-2019/12) Co-supervised with Joseph Bielawski. (Biology Dept. in Dalhousie). Statistical Approaches for Spatial-Temporal Dynamics of Microbial Communities in the Red Sea.

Junqiu Gao, MSc (2017/9-2019/8) Co-supervised with Kenney (Math. and Stat. Dept., Dalhousie). Ornstein-Uhlenbeck Process and Optimal Sampling for Analysis of Microbiome Data. Data analyst in PVSC.

Tianshu Huang, MSc (2015/9-2017/8). Co-supervised with Kenney (Math. and Stat. Dept., Dalhousie). Semi-parametric Principal Component Analysis for Poisson Count Data with Application to Microbiome Data Analysis. Data analyst in PVSC.

Hao He, MSc. (2014/9-2016/4). Co-supervised with Kenney (Math. and Stat. Dept., Dalhousie). Robust Ranking and selection with heavy-tail priors and its applications in market basket analysis.

Chongci Tang, MSc. (2014/9-2016/4). Co-supervised with Joseph Bielawski (Biology). Statistical approaches for matching the components of complex microbial communities.

Chaoyue Liu, MSc. (2014/9-2016/4). Co-supervised with Robert Beiko (Computer science). Gene clustering based on co-occurrence with correction for common evolutionary history.

Rana Bashwih, MSc. (Bioinformatics) (2013/9-2016/8). Co-supervised with Joseph Bielawski (Biology). Inference and investigation of marine microbial community structures in the global oceans.

Chang Chen, MSc. (2014/9-2016/8). Co-supervised with Robert Beiko (Computer science). Negative binomial modelling and applications for microbial count data.

Li Li, MSc (2011/9-2016/4). Co-supervised with Kenney (Math. and Stat. Dept., Dalhousie). A likelihood based clustering method for detection of recombination for DNA and Amino Acid sequences.

Yun Cai, MSc. (2013/9-2014/8 ). Co-supervised with Toby Kenney. Supervised Non-Negative Matrix Factorization for Analysis of Microbiome Data.

Michael Butler, MSc. (2013/9-2014/8 ). A hierarchical structured machine-learning method for large-scale multi-class problems. Medical doctor in Toronto.

Wei Dai, M.Sc. (2010/9-2013/8). Co-supervised with Kenney. A new test to build confidence region using balanced minimum evolution method.

Jiachi Zhu, Msc (2010-2012). Hedging the return on equity and firm profit: evidence from Canadian oil and gas companies.

Wei Chen, M.Sc. (2010-2012). Co-supervised with Joe Bielawski. The Exploration of Effect of Model Misspecification and Development of an Adequacy-Test for Substitution Model in Phylogenetics.

Caroline Urquhart, M.Sc. (2006-2011). Co-supervised with Joe Bielawski. Analysis of Prokaryotic Metabolic Networks. Business Analyst at Johnson Inc..

Mei Chen, M.Sc. (2006-2007). Co-supervised with Chris Field. Model comparisons between general time reversible model and Barry Hartigan model. Government employee, Ottawa.

Li Li, M. Sc., (2005-2006). Co-supervised with Joe Bielawski. Development of spherical data analysis techniques for phylogenomics. Ph.D. Student in Univ. of Toronto now.

Melanie Abeysundera, (2005-2006). Co-supervised with Chris Field. Predicting protein structure and functions using spectral techniques. PhD student of myself after.

Le Bao, M. Sc. (2004-2005). Co-supervised with Joe Bielawski. Generalized fixed effect models and likelihood based clustering in codon substitution models. (PhD in Univ. of Washington, and now a faculty member in Department of Statistics, Pennsylvania State University.)

Shuyan Li, M. Sc. (2004-2005). Co-supervised with Bruce Smith. Histogram-Based Mutual Information Estimation. Working in a consulting company in USA.

Chang Dan, M.Sc. (Dept. of Economics , Essay) 2004-2005. Co-supervised with Kuan Xu. Does Hedging Add Firm Value? Empirical Evidence From Canadian Oil and Gas Companies. Employed by a financial institute in China.

Krista Collins, M. Sc. 2003 -2005. Co-supervised with Chris Field. Examining the periodicity in DNA and Amino Acid sequences using the spectral envelope. Employed by Statistics Canada.

David Campbell, M.Sc. 2002 -2003. Application of Wavelets in Clustering Time Series. Faculty member in Dept. of Stat. and Actuarial Sci., Simon Fraser Univ..



Postdoc supervised:

Wei Zhou, Postdoc fellow. (2018/8-2021/9). Co-supervised with Bielawski (Biology Dept. in Dalhousie). Prediction for the upcoming cyanobacteria bloom in lakes based on the lake microbial community analysis.

Mahdi Shafiei, (2011-2012). Co-supervised with Bielawski (Biology). Network modelling of complex microbial communities.(Currently working for Google Youtube)

Honours theses:

Claire Cui (2021/9-2022/4) Fluorescence data and Stabilizing Variable Selection for Analysis of Water Treatment.

Xinyi Xie (2021/9-2022/4) Effect of trauma team activations (TTAs) and Canadian Triage and Acuity Scale 1 patients (CTAS 1) on other patients' waiting time in the emergency department.

Peiyu Zhao (2021/5-2021/12) Do Trauma Team Activations Affect Pediatric Emergency Department Crowding? 

Ziqi Zhang (2020/9-2021/5) Prediction of human body temperature and presence of fever based on thermal camera images.

Jiachen Wang (2020/9-2021/5) Gene networks related to nine potato traits by NMF. (a collaborative work).

Jiajun Ma(2020/9-2021/5) Gene networks related to nine potato traits by NMF. (a collaborative work).

Yuexu Wang (2020/9-2021/5) Gene networks for potato plants by DBSCAN clustering method. (a collaborative work).

Renny Doig (2018/9-2019/4). Prediction of multiple traits in potato plants using gene expression profiles.

Amir Farrag (2017/11-2018/4)  Data Mining for Detection of Acetabular Cartilage Delamination in Femoroacetabular Impingement Patients.

Mia Parenteau (2018/1-2018/4) Using Gene Expression as a Means to Predict Response in Potato Data.

Ying Chi (2017/8-2018/4). Principal Component Analysis of Fatty Acids in Atlantic Salmon.

Xinyue Zhang (2017/1-2017/8). GAM and ARIMA models for prediction for the patient emergency visits on different hospital sites.

Molly Hayes (2016/9-2017/4). Co-supervised with Morgan Langille. Generalization of removing unwanted variance methods for mining the metagenomics data from multiple resources.

Ziwei Jin (2016/5-2016/12) Common linear discriminant analysis (CLDA) as a prediction method by removing unwanted sources of metagenomics variance.

Qi Li (2016/5-2016/12). Time series modelling and prediction for the patient emergency visits on different hospital sites.

Yike Hou (2016/5-2016/8). Clustering analysis based on the MLE estimates of the phase and periodicity for the time series of ocean microbial marker-gene data.

Jing Zhang (2013/9 - 2014/4). Analyzing the Impact of Ocean Acidification on Bacterial Community Structure Using Clustering analysis. Risk analyst, GV Funds

Li Li (2009-2010). Testing the periodicity of annually reoccurring bacterial communities from ocean conditions. Statistical Analyst, Canadian Center for Vaccinology.

Cuiwei Luo (2009-2010). Predicting the stocks from the market indices.

Sylvia de la Ronde (2007-2008). Co-supervised with Beiko (Computer science, Dalhousie). Identifying environmental factors in lake bacteria compositions. Research and Statistical Officer, Government of Nova Scotia, Department of Labour and Advanced Education, Universities and Colleges Division.

Shuai Gao (2007-2008). Linear discriminant analysis in high dimensional space: simulation studies.

Scott Wile (2005-2006). Asymmetric adjustments in Canadian retail gasoline market. Employee of Statistics Canada.



Others:

Junqiu Gao (2019/9-2020/1). Co-supervised with Ying Zhang (Acadia Univ.) Simulation and sampling methods on multivariate time series data.

Xueli Xu (2019/8-2019/10) Visiting PhD student from Nankai Univ..

Libai Xu (2019/8-2019/9) Visiting PhD student from Nankai Univ..

Hao He (2016/5-2016/8, Research Associate). Co-supervised with Chris Field. Modelling and inference on the impact of ocean acidification on bacterial community structure with a model based two-way clustering methods.

Yanxia Sun, Mitacs Globalink summer intern. (2015/6-2015/8). Metagenomic time series analysis. MSc candidate, Peking Union Medical College in Basic Medicine.

Mengying Wu, Mitacs Globalink Program Student Placement (July. 2014-Sep. 2014). Rare Target Identification in Drug Discovery.

Nader Fallah (Visiting PhD Student, 2007-2008). Nonlinear Poisson regression using neural networks. Post-doc fellow at UBC.

Emad Bahrami Samani (2006-2007, Honours thesis supervised distantly, Amirkabir Univ. of Technology, Tehran, Iran). A Novel Hybrid GMM/SVM Architecture for Protein Secondary Structure Prediction. PhD in University of Southern California.

Le Bao (2005-2006, Research Associate). Co-supervised with Joe Bielawski. Improving the estimation of parameters in codon models.