
Aragam, B. and Zhou, Q. (2015). Concave penalized estimation of sparse Gaussian Bayesian networks.
Journal of Machine Learning Research, 16: 22732328.

Zhou, Q. (2014). Monte Carlo simulation for Lassotype problems by estimator augmentation.
Journal of the American Statistical Association, 109: 14951516.

Cha, M. and Zhou, Q. (2014). Detecting clustering and ordering binding patterns among transcription factors via point process models. Bioinformatics, 30: 22632271.

Fu, F. and Zhou, Q. (2013).
Learning sparse causal Gaussian networks with experimental intervention:
Regularization and coordinate descent.
Journal of the American Statistical Association, 108: 288300.

Zhou, Q. (2011).
Multidomain sampling with applications to structural inference of Bayesian networks.
Journal of the American Statistical Association, 106: 13171330.

Zhou, Q. (2011).
Random walk over basins of attraction to construct Ising energy landscapes.
Physical Review Letters, 106: 180602.

Sridharan, R., Tchieu, J., Mason, M.J., Yachechko, R., Kuoy, E., Horvath, S.,
Zhou, Q., and Plath, K. (2009). Role of the murine
reprogramming factors in the induction of pluripotency. Cell, 136:
364377.

Zhou, Q., Chipperfield, H., Melton, D.A., and Wong, W.H. (2007).
A gene regulatory network in mouse embryonic stem cells. Proceedings of the National Academy
of Sciences of USA, 104: 1643816443.

Kou,
S.C.*, Zhou, Q.*, and Wong, W.H. (2006). Equienergy sampler with applications in statistical
inference and statistical mechanics (with discussion). Annals of Statistics,
34: 15811652. (*Equal contribution.)

Zhou, Q. and Wong, W.H. (2004).
CisModule: De novo discovery of cisregulatory
modules by hierarchical mixture modeling. Proceedings of the National Academy of Sciences of USA,
101: 1211412119.

Zhou, Q. and Liu, J.S. (2004).
Modeling withinmotif dependence for transcription factor
binding site predictions. Bioinformatics, 20: 909916.