Publications
Group highlights
At the end of this page, you can find the full list of publications and patents. All papers are also available on arXiv.
We introduce inverse sparse regression (inspre), an approach to learning causal networks that leverages large-scale intervention-response data. Applied to 788 genes from the genome-wide perturb-seq dataset, inspre helps elucidate the network architecture of blood traits.
B.C. Brown*, J.A. Morris, T. Lappalainen, D.A. Knowles
bioRxiv 10.1101/2023.10.13.562293
We introduce multi-set correlation and factor analysis (MCFA), an unsupervised integration method tailored to the unique challenges of high-dimensional genomics data that enables fast inference of shared and private factors. Applied to 614 diverse samples, we find samples cluster strongly by ancestry even in the absence of genetic information, and identify and interpret factors related to metabolic disease.
B.C. Brown, C. Wang†, S. Kasela, F. Aguet, D.C. Nachun, K.D. Taylor, R.P. Tracy, P. Durda, Y. Liu, W.C. Johnson, D. Van Den Berg, N. Gupta, S. Gabriel, J.D. Smith, R. Gerzsten, C. Clish, Q. Wong, G. Papanicolau, T.W. Blackwell, J.I. Rotter, S.S. Rich, R.G Barr, K.G. Ardlie, D.A. Knowles, and T. Lappalainen
Cell Genom. 2023 Jul 10;3(8):100359
We develop a way to rapidly screen for putatively causal effects in biobank-scale data.
B.C. Brown and D. A. Knowles
Am J Hum Genet. 2021 Dec 2;108(12):2319-2335
We apply canonical correlation analysis to principal components of genotype and expression, revealing under-appreciate population structure in expression data.
B.C. Brown, N.L. Bray and L. Pachter
PLoS Genet. 2018 Dec 19;14(12)
We consider the cross-population genetic correlation and use it to show that complex trait genetic effect sizes can vary substantially across populations throughout the genome.
B.C. Brown, AGEN-T2D, C. Ye, A.L. Price and N. Zaitlen
Am J Hum Genet. 2016 Jul 7;99(1):76-88
Patents
Milan P Allan, S Gröblacher, RA Norte, M Leeuwenhoek
Novel atomic force microscopy probes with phononic crystals
PCT/NL20-20/050797 (2020)
Milan P Allan
Methods of manufacturing superconductor and phononic elements
US10439125B2 (2016)
Full List of publications
Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects
S. Kasela, F. Aguet, S. Kim-Hellmuth, B.C. Brown, D.C. Nachun, R.P. Tracy, P. Durda, Y. Liu, K.D. Taylor, W.C. Johnson, D. Van Den Berg, S. Gabriel, N. Gupta, J.D. Smith, T.W. Blackwell, J.I. Rotter, K.G. Ardlie, A. Manichaikul, S.S. Rich, R.G. Barr and T Lappalainen
Am J Hum Genet. 2024 Jan 4;111(1):133-149.
Large-scale causal discovery using interventional data sheds light on the regulatory network architecture of blood traits
B.C. Brown*, J.A. Morris, T. Lappalainen, D.A. Knowles
bioRxiv 10.1101/2023.10.13.562293
Multiset correlation and factor analysis enables exploratory analysis of multi-omic data
B.C. Brown, C. Wang†, S. Kasela, F. Aguet, D.C. Nachun, K.D. Taylor, R.P. Tracy, P. Durda, Y. Liu, W.C. Johnson, D. Van Den Berg, N. Gupta, S. Gabriel, J.D. Smith, R. Gerzsten, C. Clish, Q. Wong, G. Papanicolau, T.W. Blackwell, J.I. Rotter, S.S. Rich, R.G Barr, K.G. Ardlie, D.A. Knowles, and T. Lappalainen
Cell Genom. 2023 Jul 10;3(8):100359
Welch-weighted Egger regression reduces false positives due to correlated pleiotropy in Mendelian randomization.
B.C. Brown and D. A. Knowles
Am J Hum Genet. 2021 Dec 2;108(12):2319-2335
Phenome-scale causal network discovery with bidirectional mediated Mendelian randomization
B.C. Brown and D.A. Knowles
bioRxiv 10.1101/2020.06.18.160176
Comparative genetic architectures of schizophrenia in East Asian and European populations
M. Lam, C. Chen, Z. Li, A.R. Martin, J. Bryois, X. Ma, H. Gaspar, M. Ikeda, B. Benyamin, B.C. Brown, R. Liu, W. Zhou, L. Guan, Y. Kamatani, S. Kim, M. Kubo, A.A.A.A. Kusumawardhani, C. Liu, H. Ma, S. Periyasamy, A. Takahashi, Z. Xu, H. Yu, F. Zhu, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Indonesia Schizophrenia Consortium, Genetic REsearch on schizophreniA neTwork-China and the Netherlands (GREAT-CN), W.J. Chen, S. Faraone, S.J. Glatt, L. He, S.E. Hyman, H. Hwu, S.A. McCarroll, B.M. Neale, P. Sklar, D.B. Wildenauer, X. Yu, D. Zhang, B.J. Mowry, J. Lee, P. Holmans, S. Xu, P.F. Sullivan, S. Ripke, M.C. O’Donovan, M.J. Daly, S. Qin, P. Sham, N. Iwata, K.S. Hong, S.G. Schwab, W. Yue, M. Tsuang, J. Liu, X. Ma, R.S. Kahn, Y. Shi and H. Huang
Nat Genet. 2019 Dec;51(12):1670-1678
Expression reflects population structure
B.C. Brown, N.L. Bray and L. Pachter
PLoS Genet. 2018 Dec 19;14(12)
Estimating cross-population genetic correlations of causal effect sizes
K.J. Galinsky, Y.A. Reshef, H.K. Finucane, P. Loh, N. Zaitlen, N.J. Patterson, B.C. Brown and A.L. Price
Genet Epidemiol. 2019 Mar;43(2):180-188
Transethnic genetic correlation estimates from summary statistics
B.C. Brown, AGEN-T2D, C. Ye, A.L. Price and N. Zaitlen
Am J Hum Genet. 2016 Jul 7;99(1):76-88
Local joint testing improves power and identifies both missing and spurious heritability in association studies
B.C. Brown, A.L. Price, N.A. Patsopolous and N. Zaitlen
Genetics. 2016 Jul;203(3):1105-16
Adapt-Mix: Learning local genetic correlation structure improves summary statistics based analyses
D. Park, B.C. Brown, C. Eng, S. Huntsman, D. Hu, D. Torgerson, E. Burchard and N. Zaitlen
Bioinformatics. 2015 Jun 15;31(12):i181-9
Fast segment insertion and incremental construction of constrained Delaunay triangulations
J. R. Shewchuk and B.C. Brown
Comp Geom. 2015 Sept; 48(8):554-574
The Computational Difficulty of Computing the Density of States
B.C. Brown, S. T. Flammia, N. Schuch
Phys Rev Lett. 2011 Jul 22;107(4):040501
Considerations For The Optimal Polarization of 3He Targets
B.C. Brown
AIP Conf Proc. 2009; 1149:895–898