2015

Spencer, Simon E. F., Hill, Steven M. (Mark) and Mukherjee, Sach (2015) Inferring network structure from interventional time-course experiments. Annals of Applied Statistics, Volume 9 (Number 1). pp. 507-524. doi:10.1214/15-AOAS806

2014

Oates, Chris J., Dondelinger, Frank, Bayani, Nora, Korkola, James, Gray, Joe W. and Mukherjee, Sach (2014) Causal network inference using biochemical kinetics. Bioinformatics, Volume 30 (Number 17). i468-i474. doi:10.1093/bioinformatics/btu452

Casale, Francesco Paolo, Giurato, Giorgio, Nassa, Giovanni, Armond, Jonathan W., Oates, Chris J., Corá, Davide, Gamba, Andrea, Mukherjee, Sach, Weisz, Alessandro and Nicodemi, Mario (2014) Single-cell states in the estrogen response of breast cancer cell lines. PLoS ONE , 9 (2). Article number e88485. doi:10.1371/journal.pone.0088485

Armond, Jonathan W., Saha, Krishanu, Rana, Anas A., Oates, Chris J., Jaenisch, Rudolf, Nicodemi, Mario and Mukherjee, Sach (2014) A stochastic model dissects cell states in biological transition processes. Scientific Reports, Volume 4 . Article number 3692. doi:10.1038/srep03692

Oates, Chris J., Smith, J. Q., Mukherjee, Sach and Cussens, James (2014) Exact estimation of multiple directed acyclic graphs. Statistics and Computing . (Submitted)

2012

Hill, Steven M. (Mark), Lu, Y., Molina, J., Heiser, L. M., Spellman, Paul T., Speed, Terence P., Gray, Joe W., Mills, G. B. and Mukherjee, Sach (2012) Bayesian inference of signaling network topology in a cancer cell line. Bioinformatics, Vol.28 (No.21). pp. 2804-2810. doi:10.1093/bioinformatics/bts514

Hill, Steven M. (Mark), Neve, Richard M., Bayani, Nora, Kuo, Wen-Lin, Ziyad, Safiyyah, Spellman, Paul T., Gray, Joe W. and Mukherjee, Sach (2012) Integrating biological knowledge into variable selection : an empirical Bayes approach with an application in cancer biology. BMC Bioinformatics, Volume 13 (Number 1). Article no. 94. doi:10.1186/1471-2105-13-94

Oates, Chris J. and Mukherjee, Sach (2012) Network inference and biological dynamics. Annals of Applied Statistics, Vol.6 (No.3). pp. 1209-1235. doi:10.1214/11-AOAS532

Oates, Chris J., Hennessy, B. T., Lu, Y., Mills, G. B. and Mukherjee, Sach (2012) Network inference using steady-state data and Goldbeter-koshland kinetics. Bioinformatics, Vol.28 (No.18). pp. 2342-2348. doi:10.1093/bioinformatics/bts459

Nam, Christopher F. H., Mukherjee, Sach, Schilk, Marco and Mukherjee, Joybrato (2012) Statistical analysis of varieties of English. Journal of the Royal Statistical Society : Series A (Statistics in Society), Volume 176 (Number 3). pp. 777-793. doi:10.1111/j.1467-985X.2012.01062.x

2011

Mukherjee, Sach and Hill, Steven M. (Mark) (2011) Network clustering : probing biological heterogeneity by sparse graphical models. Bioinformatics, Vol.27 (No.7). pp. 994-1000. doi:10.1093/bioinformatics/btr070

Goudie, Robert J. B., Mukherjee, Sach and Griffiths, Frances (2011) Exploratory network analysis of large social science questionnaires. In: Proceedings of the 8th Bayesian Modelling Applications Workshop, Barcelona, Spain, 14th July 2011. Published in: The 8th Bayesian Modelling Applications Workshop pp. 34-42.

2010

Barker, D., Hill, Steven M. (Mark) and Mukherjee, Sach (2010) MC(4): a tempering algorithm for large-sample network inference. In: 5th International Conference on Pattern Recognition in Bioinformatics, Nijmegen, The Netherlands, 22-24 Sep 2010. Published in: Pattern Recognition in Bioinformatics, Volume 6282 pp. 431-442. ISSN 0302-9743. doi:10.1007/978-3-642-16001-1_37

2009

Kiddle, Steven J., Windram, Oliver P., McHattie, Stuart, Mead, A. (Andrew), Beynon, Jim, Buchanan-Wollaston, Vicky, Denby, Katherine J. and Mukherjee, Sach (2009) Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana. Bioinformatics, Vol.26 (No.3). pp. 355-362. doi:10.1093/bioinformatics/btp673

Mukherjee, Sach, Pelech, Steven, Neve, Richard M., Kuo, Wen-Lin, Ziyad, Safiyyah, Spellman, Paul T., Gray, Joe W. and Speed, Terence P. (2009) Sparse combinatorial inference with an application in cancer biology. Bioinformatics, Vol.25 (No.2). pp. 265-271. doi:10.1093/bioinformatics/btn611

2008

Mukherjee, Sach and Speed, T. P. (2008) Network inference using informative priors. Proceedings of the National Academy of Sciences of the United States of America, Vol.105 (No.38). pp. 14313-14318. doi:10.1073/pnas.0802272105