Article

Ensembles of lasso screening rules.
Lee, S., Görnitz, N., Xing, E.P., Heckerman, D. and Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556
IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (12): 2841-2852. 24 November 2017

Profiling of short-tandem-repeat disease alleles in 12,632 human whole genomes.
Tang, H., Kirkness, E.F., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Biggs, W.H., Fabani, M., Guzman, E., Ramakrishnan, S., Lavrenko, V., Kakaradov, B., Hou, C., Hicks, B., Heckerman, D., Och, F.J., Caskey, C.T., Venter, J.C. and Telenti, A.
American Journal of Human Genetics 101 (5): 700-715. 2 November 2017

Sparse probit linear mixed model.
Mandt, S. ORCID: https://orcid.org/0000-0001-7836-7839, Wenzel, F., Nakajima, S., Cunningham, J., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556 and Kloft, M.
Machine Learning 106 (9-10): 1621-1642. October 2017

Identification of individuals by trait prediction using whole-genome sequencing data.
Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Sabatini, R., Maher, M.C., Kang, E.Y., Lee, S., Arikan, O., Harley, A., Bernal, A., Garst, P., Lavrenko, V., Yocum, K., Wong, T., Zhu, M., Yang, W.Y., Chang, C., Lu, T., Lee, C.W.H., Hicks, B., Ramakrishnan, S., Tang, H., Xie, C., Piper, J., Brewerton, S., Turpaz, Y., Telenti, A., Roby, R.K., Och, F.J. and Venter, J.C.
Proceedings of the National Academy of Sciences of the United States of America 114 (38): 10166-10171. 19 September 2017

easyGWAS: a cloud-based platform for comparing the results of genome-wide association studies.
Grimm, D.G. ORCID: https://orcid.org/0000-0003-2085-4591, Roqueiro, D., Salomé, P.A., Kleeberger, S., Greshake, B. ORCID: https://orcid.org/0000-0002-9925-9623, Zhu, W., Liu, C., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Stegle, O., Schölkopf, B., Weigel, D. ORCID: https://orcid.org/0000-0002-2114-7963 and Borgwardt, K.M. ORCID: https://orcid.org/0000-0001-7221-2393
Plant Cell 29 (1): 5-19. January 2017

Efficient set tests for the genetic analysis of correlated traits.
Casale, F.P., Rakitsch, B., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556 and Stegle, O.
Nature Methods 12 (8): 755-758. August 2015

Computational and statistical issues in personalized medicine.
Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556 and Hackerman, D.
XRDS: Crossroads, The ACM Magazine for Students 21 (4): 24-27. 27 July 2015

Accurate liability estimation improves power in ascertained case-control studies.
Weissbrod, O., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Geiger, D. and Heckerman, D.
Nature Methods 12 (4): 332-334. April 2015

Greater power and computational efficiency for kernel-based association testing of sets of genetic variants.
Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Xiang, J., Horta, D., Widmer, C., Kadie, C., Heckerman, D. and Listgarten, J.
Bioinformatics 30 (22): 3206-3214. 15 November 2014

Further improvements to linear mixed models for genome-wide association studies.
Widmer, C., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Weissbrod, O., Fusi, N., Kadie, C., Davidson, R., Listgarten, J. and Heckerman, D.
Scientific Reports 4 : 6874. 12 November 2014

Warped linear mixed models for the genetic analysis of transformed phenotypes.
Fusi, N., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Lawrence, N.D. ORCID: https://orcid.org/0000-0001-9258-1030 and Stegle, O. ORCID: https://orcid.org/0000-0002-8818-7193
Nature Communications 5 : 4890. 19 September 2014

Quantifying the uncertainty in heritability.
Furlotte, N.A., Heckerman, D. and Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556
Journal of Human Genetics 59 (5): 269-275. May 2014

Epigenome-wide association studies without the need for cell-type composition.
Zou, J., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Heckerman, D., Aryee, M. ORCID: https://orcid.org/0000-0002-6848-1344 and Listgarten, J.
Nature Methods 11 (3): 309-311. March 2014

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control.
Bartha, I., Carlson, J.M., Brumme, C.J. ORCID: https://orcid.org/0000-0003-2722-5288, McLaren, P.J., Brumme, Z.L., John, M., Haas, D.W., Martinez-Picado, J. ORCID: https://orcid.org/0000-0002-4916-2129, Dalmau, J., López-Galíndez, C. ORCID: https://orcid.org/0000-0002-2324-9584, Casado, C., Rauch, A., Günthard, H.F. ORCID: https://orcid.org/0000-0002-1142-6723, Bernasconi, E., Vernazza, P., Klimkait, T., Yerly, S., O'Brien, S.J. ORCID: https://orcid.org/0000-0001-7353-8301, Listgarten, J., Pfeifer, N. ORCID: https://orcid.org/0000-0002-4647-8566, Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Fusi, N., Kutalik, Z., Allen, T.M., Müller, V. ORCID: https://orcid.org/0000-0001-8212-4880, Harrigan, P.R., Heckerman, D., Telenti, A. and Fellay, J. ORCID: https://orcid.org/0000-0002-8240-939X
eLife 2 : e01123. 29 October 2013

A powerful and efficient set test for genetic markers that handles confounders.
Listgarten, J., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Kang, E.Y., Xiang, J., Kadie, C.M. and Heckerman, D.
Bioinformatics 29 (12): 1526-1533. 15 June 2013

Detecting regulatory gene-environment interactions with unmeasured environmental factors.
Fusi, N., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Borgwardt, K., Lawrence, N.D. ORCID: https://orcid.org/0000-0001-9258-1030 and Stegle, O. ORCID: https://orcid.org/0000-0002-8818-7193
Bioinformatics 29 (11): 1382-1389. 1 June 2013

The benefits of selecting phenotype-specific variants for applications of mixed models in genomics.
Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Quon, G., Kang, E.Y., Kadie, C.M., Listgarten, J. and Heckerman, D.
Scientific Reports 3 : 1815. 9 May 2013

Patterns of methylation heritability in a genome-wide analysis of four brain regions.
Quon, G., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Heckerman, D. and Listgarten, J.
Nucleic Acids Research 41 (4): 2095-2104. 1 February 2013

An exhaustive epistatic SNP association analysis on expanded Wellcome Trust data.
Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Listgarten, J., Davidson, R.I., Baxter, J., Poon, H., Kadie, C.M. and Heckerman, D.
Scientific Reports 3 : 1099. 22 January 2013

A Lasso multi-marker mixed model for association mapping with population structure correction.
Rakitsch, B., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Stegle, O. ORCID: https://orcid.org/0000-0002-8818-7193 and Borgwardt, K.
Bioinformatics 29 (2): 206-214. 15 January 2013

Extraneous markers used for genetic similarity leads to loss of power in GWAS and heritability determination.
Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Quon, G., Listgarten, J. and Heckerman, D.
3 December 2012

FaST linear mixed models for genome-wide association studies.
Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Listgarten, J., Liu, Y., Kadie, C.M., Davidson, R.I. and Heckerman, .
Nature Methods 8 (10): 833-835. 4 September 2011

Whole-genome sequencing of multiple Arabidopsis thaliana populations.
Cao, J., Schneeberger, K., Ossowski, S. ORCID: https://orcid.org/0000-0002-7416-9568, Guenther, T. ORCID: https://orcid.org/0000-0001-9460-390X, Bender, S., Fitz, J., Koenig, D. ORCID: https://orcid.org/0000-0002-1037-5346, Lanz, C., Stegle, O. ORCID: https://orcid.org/0000-0002-8818-7193, Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Wang, X., Ott, F., Mueller, J., Alonso-Blanco, C. ORCID: https://orcid.org/0000-0002-4738-5556, Borgwardt, K., Schmid, K.J. and Weigel, D. ORCID: https://orcid.org/0000-0002-2114-7963
Nature Genetics 43 (10): 956-963. 28 August 2011

Efficient inference in matrix-variate Gaussian models with iid observation noise.
Stegle, O., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Mooij, J., Lawrence, N. and Borgwardt, K.
Advances in Neural Information Processing Systems 24 : 1-9. 2011

Gene function prediction from synthetic lethality networks via ranking on demand.
Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Ghahramani, Z. and Borgwardt, K.M.
Bioinformatics 26 (7): 912-918. 1 April 2010

A kernel method for unsupervised structured network inference.
Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Stegle, O., Ghahramani, Z. and Borgwardt, K.M.
Journal of Machine Learning Research 5 : 368-375. 2009

Relation prediction in multi-relational domains using matrix factorization.
Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Weber, S.H., Huang, Y., Tresp, V., Schubert, M. and Kriegel, H.P.
Proceedings of the NIPS 2008 Workshop 2008

Conference or Workshop Item

Separating sparse signals from correlated noise in binary classification.
Mandt, S., Wenzel, F., Nakajima, S., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556 and Kloft, M.
In: 2016 UAI Workshop on Causation: Foundation to Application, UAI-CFA, 29 June 2016, Jersey City, United States. 2016

Finding sparse features in strongly confounded medical binary data.
Mandt, S., Wenzel, F., Nakajima, S., Cunningham, J., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556 and Kloft, M.
In: NIPS Workshop on Machine Learning in Healthcare. 2015

It is all in the noise: efficient multi-task Gaussian process inference with structured residuals.
Rakitsch, B., Lippert, C., Borgwardt, K. and Stegle, O.
In: 27th Annual Conference on Neural Information Processing Systems, 5-10 Dec 2013, Lake Tahoe, United States of America. December 2013

Relational models for generating labeled real-world graphs.
Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Shervashidze, N. and Stegle, O.
In: 7th International Workshop on Mining and Learning with Graphs, 2-4 July 2009, Leuven, Belgium. 2009

Review

Deep learning of genomic variation and regulatory network data.
Telenti, A., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Chang, P.C. and DePristo, M.
Human Molecular Genetics 27 (R1): R63-R71. 1 May 2018

Letter

FaST-LMM-Select for addressing confounding from spatial structure and rare variants.
Listgarten, J., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556 and Heckerman, D.
Nature Genetics 45 (5): 470-471. May 2013

Improved linear mixed models for genome-wide association studies.
Listgarten, J., Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Kadie, C.M., Davidson, R.I., Eskin, E. and Heckerman, D.
Nature Methods 9 (6): 525-526. 30 May 2012

Preprint

No major flaws in "Identification of individuals by trait prediction using whole-genome sequencing data".
Lippert, C. ORCID: https://orcid.org/0000-0001-6363-2556, Sabatini, R., Maher, M.C., Kang, E.Y., Lee, S., Arikan, O., Harley, A., Bernal, A., Garst, P., Lavrenko, V., Yocum, K., Wong, T.M., Zhu, M., Yang, W.Y.n, Chang, C., Hicks, B., Ramakrishnan, S., Tang, H., Xie, C., Brewerton, S., Turpaz, Y., Telenti, A., Roby, R.K., Och, F. and Venter, J.C.
bioRxiv : 187542. 19 October 2017