2018

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

2017

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

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

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

2016

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

2015

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

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

2014

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

2013

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

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

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

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

2012

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

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

2011

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

2010

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

2009

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

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

2008

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