Zhao S, Engelhardt BE, Mukherjee S, and Dunson DB. "Fast moment estimation for generalized latent Dirichlet models" *Journal of the American Statistical Association (JASA)* [pdf]

The MELD software, written and maintained by Shiwen Zhao, is publicly available: [Software]

Darnell G, Georgiev S, Mukherjee S, and Engelhardt, BE. "Adaptive randomized dimension reduction on massive data" *Journal of Machine Learning Research (JMLR)* [pdf]

The ARSVD software, written and maintained by Gregory Darnell, is publicly available: [Software]

Zhao S, Gao C, Mukherjee S, and Engelhardt BE. "Bayesian group latent factor analysis with structured sparsity" *Journal of Machine Learning Research (JMLR)* [pdf]

The BASS software, written and maintained by Shiwen Zhao, is publicly available: [Software]

Gao C, Zhao S, McDowell IC, Brown CD, and Engelhardt BE. "Differential gene co-expression networks via Bayesian biclustering models" *(submitted)* [arXiv]

The BicMix software, written and maintained Dr. Chuan Gao, is publicly available: [Software]; send questions and comments to: chuan.gao@duke.edu

Engelhardt BE, and Adams RP. "Bayesian structured sparsity from Gaussian fields" *(in review)* [ArXiV]

The software is available on GitHub [Software]

Mimno D, Blei DM, and Engelhardt BE. "Posterior predictive checks to quantify lack-of-fit in admixture models of latent population structure" *(in review)* [ArXiV]

The software is available on GitHub [Software]

These methods and results are described in the paper:

Zhang W, Spector TD, Deloukas P, Bell JT, and Engelhardt BE. "Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory element" *(accepted)* [ArXiv]

The methylation data from the Methylation 450K array on 100 individuals from the TwinsUK consortium described and analyzed in this paper have also been posted online at Gene Expression Omnibus with ID GSE62992: [Data]

Gao C, Brown CD, and Engelhardt BE. "A latent factor model with a mixture of sparse and dense factors to model gene expression data with confounding effects" *Submitted.* [ArXiV]

Download C++ code, instructions, and documentation for SFAmix 1.0.

Brown CD, Mangravite LM, Engelhardt BE (2013). "Integrative modeling of eQTLs and cis-regulatory elements suggests mechanisms underlying cell type specificity of eQTLs" *PLoS Genetics* 9(8): e1003649. [PDF]

One change from the pipeline noted above is that we include genotypes imputed using Impute2 software with prephasing, and we impute up to the 1000 Genomes reference data from March 2012, and we do not filter low MAF SNPs. Note that the resulting imputed genotype files are in CHIAMO format.

Engelhardt BE, Stephens M (2010) "Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis." *PLoS Genetics* 6(9):e1001117.

Download C++ code and instructions for SFA 1.0 and further documentation for the SFA model.

Engelhardt BE, Jordan MI, Srouji JR, and Brenner SE (2011) Genome-scale phylogenetic function annotation of large and diverse protein families. Genome Research (*in press*).