Publications

Preprints and Unpublished Work
Bianca Dumitrascu, Gregory Darnell, Julien Ayroles, Barbara E Engelhardt. A Bayesian test to identify variance effects, arXiv preprint arXiv:1512.01616. [bibtex] [pdf]
Ashlee Valente, Geoffrey Ginsburg, Barbara E Engelhardt. Nonparametric reduced-rank regression for multi-SNP, multi-trait association mapping, arXiv preprint arXiv:1512.02306. [bibtex] [pdf]
Mehmet E Basbug, Barbara E Engelhardt. Clustering with beta divergences, arXiv preprint arXiv:1510.05491. [bibtex] [pdf]
Mehmet E Basbug, Barbara E Engelhardt. Coupled compound Poisson factorization, arXiv preprint arXiv:1701.02058. [bibtex] [pdf]
Barbara E Engelhardt, Ryan P Adams. Bayesian Structured Sparsity from Gaussian Fields, arXiv preprint arXiv:1407.2235, 1. [bibtex] [pdf]
Shiwen Zhao, Barbara E Engelhardt, Sayan Mukherjee, David B Dunson. Fast moment estimation for generalized latent Dirichlet models, arXiv preprint arXiv:1603.05324. [bibtex] [pdf]
Sanvesh Srivastava, Barbara E Engelhardt, David B Dunson. Expandable Factor Analysis, arXiv preprint arXiv:1407.1158. [bibtex] [pdf]
Ashis Saha, Yungil Kim, Ariel D. H. Gewirtz, Brian Jo, Chuan Gao, Ian C. McDowell, GTEx Consortium, Barbara E. Engelhardt, Alexis Battle. Co-expression networks reveal the tissue-specific regulation of transcription and splicing, bioRXiv preprint 078741. [bibtex] [pdf]
Gautam Sabnis, Debdeep Pati, Barbara E Engelhardt, Natesh Pillai. A divide and conquer strategy for high dimensional Bayesian factor models, arXiv preprint arXiv:1612.02875. [bibtex] [pdf]
Ian C McDowell, Athma A Pai, Cong Guo, Christopher M Vockley, Christopher D Brown, Tim E Reddy, Barbara E Engelhardt. Many long intergenic non-coding RNAs distally regulate mRNA gene expression levels, bioRXiv preprint 044719. [bibtex] [pdf]
Brian Jo, Yuan He, Benjamin J. Strober, Princy Parsana, Francois Aguet, Andrew A. Brown, Stephane E. Castel, Eric R. Gamazon, Ariel Gewirtz, Genna Gliner, Buhm Han, Amy Z. He, Eun Yong Kang, Ian C. McDowell, Xiao Li, Pejman Mohammadi, Christine B. Peterson, Gerald Quon, Ashis Saha, Ayellet V. Segré, Jae Hoon Sul, Timothy J. Sullivan, Kristin G. Ardlie, Christopher D. Brown, Donald F. Conrad, Nancy J. Cox, Emmanouil T. Dermitzakis, Eleazar Eskin, Manolis Kellis, Tuuli Lappalainen, Chiara Sabatti, GTEx Consortium, Barbara E. Engelhardt, Alexis Battle. Distant regulatory effects of genetic variation in multiple human tissues, bioRXiv preprint 074419. [bibtex] [pdf]
Chuan Gao, Christopher D Brown, Barbara E Engelhardt. A latent factor model with a mixture of sparse and dense factors to model gene expression data affected by technical and biological covariates, arXiv preprint arXiv:1310.4792. [bibtex] [pdf]
Refereed Articles
2017
Ghassen Jerfel, Mehmet E Basbug, Barbara E Engelhardt. Dynamic collaborative filtering with compound Poisson factorization, Proceedings of the Artificial Intelligence and Statistics (AISTATS) Conference (accepted), 2017. [bibtex] [pdf]
Gregory Darnell, Stoyan Georgiev, Sayan Mukherjee, Barbara E Engelhardt. Adaptive randomized dimension reduction on massive data, Journal of Machine Learning Research (JMLR, accepted), 2017. [bibtex] [pdf]
Peter D Tonner, Cynthia D Darnell, Barbara E Engelhardt, Amy Schmid. Detecting differential growth of microbial populations with Gaussian process regression, Genome Research (accepted), 2017. [bibtex] [pdf]
2016
Mehmet E Basbug, Barbara E Engelhardt. Hierarchical compound Poisson factorization, Proceedings of the International Conference on Machine Learning, 2016. [bibtex] [pdf]
Shiwen Zhao, Chuan Gao, Sayan Mukherjee, Barbara E Engelhardt. Bayesian group latent factor analysis with structured sparse priors, Journal of Machine Learning Research (JMLR), 2016. [bibtex] [pdf]
Chuan Gao, Shiwen Zhao, Ian C McDowell, Christopher D Brown, Barbara E Engelhardt. Context-specific and differential gene co-expression networks via Bayesian biclustering models, PLOS Computational Biology, 12, 2016. [bibtex] [pdf]
2015
Genetics of Personality Consortium. Meta-analysis of genome-wide association studies for neuroticism, and the polygenic association with major depressive disorder, JAMA Psychiatry, 72(7):642-650, 2015. [bibtex] [pdf] [doi]
Weiwei Zhang, Tim Spector, Panos Deloukas, Jordana Bell, Barbara E Engelhardt. Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements, Genome Biology, 16(1):14, 2015. [bibtex] [pdf] [doi]
Stephanie M van Den Berg, Marleen HM de Moor, Karin JH Verweij, Robert F Krueger, Michelle Luciano, Alejandro Arias Vasquez, Lindsay K Matteson, Jaime Derringer, Tõnu Esko, Najaf Amin, others. Meta-analysis of genome-wide association studies for extraversion: Findings from the Genetics of Personality Consortium, Behavior Genetics, Springer, 2015. [bibtex] [pdf] [doi]
David Mimno, David M Blei, Barbara E Engelhardt. Posterior predictive checks to quantify lack-of-fit in admixture models of latent population structure, Proceedings of the National Academy of Sciences, 112(26):E3341–50, 2015. [bibtex] [pdf] [doi]
Barbara E Engelhardt, Christopher D Brown. Diving deeper to predict noncoding sequence function, Nature Methods (News & Views; not peer-reviewed), Nature Publishing Group, 12(10):925–926, 2015. [bibtex] [pdf]
2014
Amy B Hart, Eric R Gamazon, Barbara E Engelhardt, Pamela Sklar, Anna K Kähler, Christina M Hultman, Patrick F Sullivan, Benjamin M Neale, Stephen V Faraone, Harriet de Wit, Nancy J Cox, Abraham a Palmer. Genetic variation associated with euphorigenic effects of d-amphetamine is associated with diminished risk for schizophrenia and attention deficit hyperactivity disorder, Proceedings of the National Academy of Sciences of the United States of America, 111(16):5968–73, 2014. [bibtex] [pdf] [doi]
2013
Lara M Mangravite*, Barbara E Engelhardt*, Marisa W Medina, Joshua D Smith, Christopher D Brown, Daniel I Chasman, Brigham H Mecham, Bryan Howie, Heejung Shim, Devesh Naidoo, QiPing Feng, Mark J Rieder, Yii-Der I Chen, Jerome I Rotter, Paul M Ridker, Jemma C Hopewell, Sarah Parish, Jane Armitage, Rory Collins, Russell A Wilke, Deborah A Nickerson, Matthew Stephens, Ronald M Krauss. A statin-dependent QTL for GATM expression is associated with statin-induced myopathy, Nature, 502(7471):377–80, 2013. [bibtex] [pdf] [doi]
Fantine Mordelet, John Horton, Alexander J Hartemink, Barbara E Engelhardt, Raluca Gordân. Stability selection for regression-based models of transcription factor-DNA binding specificity., Bioinformatics, 29(13):i117–25, 2013. [bibtex] [pdf] [doi]
Christopher D Brown, Lara M Mangravite, Barbara E Engelhardt. Integrative modeling of eQTLs and cis-regulatory elements suggests mechanisms underlying cell type specificity of eQTLs., PLoS Genetics, 9(8):e1003649, 2013. [bibtex] [pdf] [doi]
Kathryn E Muratore, Barbara E Engelhardt, John R Srouji, Michael I Jordan, Steven E Brenner, Jack F Kirsch. Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: Recurrence of tyrosine aminotransferase activity in the I$\alpha$ subfamily, Proteins: Structure, Function, and Bioinformatics, Wiley Online Library, 81(9):1593–1609, 2013. [bibtex] [pdf]
2012
Amy B Hart*, Barbara E Engelhardt*, Margaret C Wardle, Greta Sokoloff, Matthew Stephens, Harriet de Wit, Abraham Palmer.Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13)., PLoS One, 7(8):e42646, 2012. [bibtex] [pdf] [doi]
2011
Barbara E Engelhardt, Michael I Jordan, John R Srouji, Steven E Brenner. Genome-scale phylogenetic function annotation of large and diverse protein families., Genome Research, 21(11):1969–80, 2011. [bibtex] [pdf] [doi]
2010
Barbara E Engelhardt, Matthew Stephens. Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis., PLoS Genetics, 6(9):e1001117, 2010. [bibtex] [pdf] [doi]
Joseph K Pickrell, John C Marioni, Athma A Pai, Jacob F Degner, Barbara E Engelhardt, Everlyne Nkadori, Jean-Baptiste Veyrieras, Matthew Stephens, Yoav Gilad, Jonathan K Pritchard. Understanding mechanisms underlying human gene expression variation with RNA sequencing, Nature, 464(7289):768–772, 2010. [bibtex] [pdf] [doi]
2005
Barbara E Engelhardt, Michael I Jordan, Kathryn E Muratore, Steven E Brenner. Protein molecular function prediction by Bayesian phylogenomics., PLoS Computational Biology, 1(5):e45, 2005. [bibtex] [pdf] [doi]
Refereed Conference Papers
2006
Barbara E Engelhardt, Michael I Jordan, Steven E Brenner. A graphical model for predicting protein molecular function, Proceedings of the 23rd International Conference on Machine Learning, ACM Press, 2006. [bibtex] [pdf] [doi]

* indicates equal authorship