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Associate Professor of Statistical Science
and Computer Science


Computational Biology & Bioinformatics
Structural Biology & Biophysics
Duke Center for Systems Biology


Duke University

  
  
 
 
 
 
 
 
Graduate Students and Postdocs

Information for prospective students and postdocs - outside Duke.

Advice for Duke students interested in joining my group.

 

Current:

  • Kevin Wiehe (Post-doctoral Fellow): Structural biology of HIV broadly-neutralizing antibodies

  • Chris Challis (PhD student, Statistics): Stochastic Models of Protein Structure Evolution

  • David McClure (PhD student, Statistics): Stochastic Object Matching in Images

  • Michael Seo (Undergrad honors thesis, Statistics): MCMC for Bayesian Classification Trees

Current rotation students:
Other students I co-advise or work closely with:

  • Jianyu Wang (PhD student, Statistics): Adaptive MCMC

  • Rolando Estrada (PhD student, CS): Probabilistic Modeling/Segmentation of Trees in Images

  • Marshall Thompson (PhD student, UPGG). Modeling post-transcriptional regulation networks.


Past:

  • Ben Cooke (PhD 2008, Mathematics). Theory and Practice in Replica-Exchange Molecular Dynamics. Now Assistant Director, Duke University Academic Skills Instruction Program.

  • Dawn Woodard (PhD 2007). Conditions for Rapid and Torpid Mixing of Parallel and Simulated Tempering on Multimodal Distributions. Now Assistant Professor of Operations Research and Information Engineering, Cornell University.

  • Joe Lucas (PhD 2006). Sparsity Modeling for High Dimensional Systems: Applications in Genomics and Structural Biology (co-advised with Mike West). Now Research Assistant Professor, Duke Institute of Genome Science & Policy.

  • Huidong Xu (MS 2009). Modeling Stochastic Switching of Electric Field Distributions in Semiconductor Superlattices. PhD Physics. Now at BlackRock.

  • Botao Jia (MS 2009). Duke Free Electron Laser Storage Ring Beam Energy Spread Analysis. Currently: PhD candidate, Physics.

  • Xiang Zhou (MS 2009). Parameter Estimation in Ising and Potts Models with Applications to Computational Protein Design. PhD Neurobiology. Now Postdoctoral Researcher in Matthew Stephens' lab, University of Chicago.

  • Jieru Zheng (MS 2006). Quantitative Structure-Activity Relationship (QSAR) Studies of MHC-Peptide Binding. PhD Chemistry. Now at Michael Allen Co.

  • Michael Seo (BS 2011). Improved MCMC Sampling for Bayesian CART. Honors thesis, high distinction.

 
Committees

 

PhD Thesis Committees:
  • Jianyang (Michael) Zeng, Computer Science, advisor Bruce Donald
  • Roy Hughes, Biochemistry, advisor Terry Oas
  • Kyle Roberts, Computational Biology & Bioinformatics, advisor Bruce Donald
  • Marshall Thompson, Genetics & Genomics, Duke University, advisor Jack Keene
  • Faisal Reza, Computational Biology & Bioinformatics, Duke University, advisor Jingdong Tian
  • Jarad Niemi, PhD 2009, Statistical Science, Duke University, advisor Mike West
  • Ivelin Georgiev, PhD 2009, Computer Science, Duke University, advisor Bruce Donald
  • Tingting Jiang, PhD 2007, Computer Science, Duke University, advisor Carlo Tomasi
  • Juliette Colinas, PhD 2006, Biology, Duke University, advisor Philip Benfey
  • Alexei Valiaev, PhD 2006, Mechanical Engineering & Materials Science, Duke University, advisor Stefan Zauscher

MS and Prelim Committees:
  • Roy Hughes, PhD student, Biochemistry (Prelim committee)
  • Kyle Roberts, PhD student, Computational Biology & Bioinformatics (Prelim committee)
  • Jianyang (Michael) Zheng, PhD student, Computer Science (Prelim committee)
  • Pablo Gainza, PhD student, Computer Science (2nd year project committee)
  • Zhenglei Gao, MS 2008, Statistical Science, Duke University (MS committee)
  • Nihshanka Debroy, PhD student, Computer Science (2nd year project advisor)
  • Jarad Niemi, PhD student, Statistical Science (Prelim committee)
  • Faisal Reza, PhD student, Biomedical Engineering (Prelim committee)
  • Zhi Ouyang, PhD student, ISDS (Prelim committee)
  • Bei Wang, PhD student, Computer Science (2nd year project committee)
  • Jen-Hwa Chu, PhD student, ISDS (Prelim committee)
  • Merrill Liechty, PhD student, ISDS (Prelim committee)
  • Ming Liao, PhD student, ISDS (Prelim committee)
  • Hui Huang, MS student, ISDS (MS committee)
  • Philippe Luedi, MS student, ISDS (MS committee)
  • Ning Li, MS 2002, Statistics & Decision Sciences; PhD 2002 Fuqua School of Business (MS committee)

ISDS and CBB First-year advising:
  • Danilo Lopes (Statistics)
  • Elena Edelman (BGT)
  • Janine Wilcox (ISDS)
  • Curtis Layton (BGT)
  • Eric Vance (ISDS)
  • Philippe Luedi (ISDS)

Undergraduate research advising:
  • Michael Seo (BS 2011). Improved MCMC Sampling for Bayesian CART. Honors thesis, high distinction.
  • Daniel Greenblatt, undergraduate student, Computer Science (2001-2)

Rotation students and RAs:
  • Hongxia Yang (StatSci)
  • Nishanka Debroy (CS)
  • Hsiang-Yu Yuan (CBB)
  • Rui Wang (CBB)
  • Abel Rodriguez (ISDS)
  • Haige Shen (CBB)