Publications

Selected publications and preprints

Nadig, A., Fu, J., Satterstrom, F.K. et al. (2026). Estimating the contribution of coding mutations to autism. medRxiv.

Shen, A., Wang, X., Mancuso, N., & O'Connor, L.J. (2026). Highly efficient genotype compression leveraging genealogical relatedness. bioRxiv.

Salehi Nowbandegani, P., Zhang, S., Hu, H., Li, H., & O'Connor, L.J. (2026). Defining and cataloging variants in pangenome graphs. Cell Genomics, 101327.

O'Connor, L.J., & Sella, G. (2026). Principled measures and estimates of trait polygenicity. The American Journal of Human Genetics, 113(6), 1347–1356.

Li, H., Kamath, T., Mazumder, R., Lin, X., & O'Connor, L.J. (2026). Improved heritability partitioning and enrichment analyses using summary statistics with graphREML. Nature Genetics, 58(7), 1573–1582.

Nadig, A., Replogle, J.M., Pogson, A.N. et al. (2025). Transcriptome-wide analysis of differential expression in perturbation atlases. Nature Genetics, 57(5), 1228–1237.

Salehi Nowbandegani, P.*, Wohns, A.W.*, Ballard, J.L., Lander, E.S., Bloemendal, A., Neale, B.M., & O'Connor, L.J. (2023). Extremely sparse models of linkage disequilibrium in ancestrally diverse association studies. Nature Genetics, 55(9), 1494–1502.

Weiner, D.J.*, Nadig, A.*, Jagadeesh, K.A., Dey, K.K., Neale, B.M., Robinson, E.B., Karczewski, K.J. & O’Connor, L.J. (2023). Polygenic architecture of rare coding variation across 394,783 exomes. Nature, 614, 492-499.

Ballard, J.L., & O'Connor, L.J. (2022). Shared components of heritability across genetically correlated traits. The American Journal of Human Genetics, 109(6), 989-1006.

Weiner, D. J., Gazal, S., Robinson, E. B., & O’Connor, L. J. (2022). Partitioning gene-mediated disease heritability without eQTLs. The American Journal of Human Genetics, 109(3), 405-416.

O’Connor, L.J. (2021). The distribution of common-variant effect sizes. Nature Genetics, 53, 1243–1249.

O'Connor, L. J., Schoech, A. P., Hormozdiari, F., Gazal, S., Patterson, N., & Price, A. L. (2019). Extreme Polygenicity of Complex Traits Is Explained by Negative Selection. The American Journal of Human Genetics, 105(3), 456-476.

O’Connor, L.J., Price, A.L. (2018). Distinguishing genetic correlation from causation across 52 diseases and complex traits. Nature Genetics, 50, 1728–1734.

Other publications and preprints

Westerman, K.E., Gervis, J.E., O'Connor, L.J., Udler, M.S., & Manning, A.K. (2026). Polygenic scores capture genetic modification of the adiposity-cardiometabolic risk factor relationship. Cell Genomics, 6(3), 101075.

O'Connor, L.J. (2026). Self-Programmed Execution for Language-Model Agents. arXiv:2605.06898 [cs.AI].

Lu, W., Chen, S., Posthuma, D., Neale, B. M., O’Connor, L. J., & Karczewski, K. J. (2024). Effect heterogeneity reveals complex pleiotropic effects of rare coding variants. bioRxiv, 2024-10.

Gazal, S., Weissbrod, O., Hormozdiari, F., Dey, K. K., Nasser, J., Jagadeesh, K. A., ..., O'Connor, L.J.,... & Price, A. L. (2022). Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity. Nature Genetics, 54, 827-836.

Weiner, D., Ling, E., Erdin, S., Tai, D. J., Yadav, R., Grove, J., ..., O'Connor, L.J.,... & Robinson, E.B. (2022). Statistical and functional convergence of common and rare variant risk for autism at chromosome 16p. Nature Genetics, 54, 1630-1639.
Yao, D. W., O'Connor, L. J., Price, A. L., & Gusev, A. (2020). Quantifying genetic effects on disease mediated by assayed gene expression levels. Nature Genetics, 52, 626-633.
O’Connor, L. J., M. Medard, & S. Feizi. Maximum Likelihood Latent Space Embedding of Logistic Random Dot Product Graphs (2020). Association for the Advancement of Artificial Intelligence.
Tin, A., Marten, J., Kuhns, V. L. H., Li, Y., Wuttke, M., Kirsten, H.,… O’Connor, L. J.,... & Kottgen, A. (2019). Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels. Nature Genetics, 51(10), 1459-1474.
Schoech, A. P., Jordan, D. M., Loh, P. R., Gazal, S., O’Connor, L. J., Balick, D. J., ... & Price, A. L. (2019). Quantification of frequency-dependent genetic architectures in 25 UK Biobank traits reveals action of negative selection. Nature communications, 10(1), 790.
Kim, S. S., Dai, C., Hormozdiari, F., van de Geijn, B., Gazal, S., Park, Y., ... O’Connor, L. J., … & Price, A.L. (2019). Genes with high network connectivity are enriched for disease heritability. The American Journal of Human Genetics, 104(5), 896-913.
Zhu, Z., Guo, Y., Shi, H., Liu, C. L., Panganiban, R. A., Chung, W., ... O’Connor, L. J., … & Liang, L. (2019). Shared genetic and experimental links between obesity-related traits and asthma subtypes in UK Biobank. Journal of Allergy and Clinical Immunology.
Reshef, Y. A., Finucane, H. K., Kelley, D. R., Gusev, A., Kotliar, D., Ulirsch, J. C., ... O’Connor, L. J., … & Price, A. L. (2018). Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk. Nature genetics, 50(10), 1483.
Hormozdiari, F., Gazal, S., van de Geijn, B., Finucane, H. K., Ju, C. J. T., Loh, P. R., … O’Connor, L. J., ... & Price, A.L. (2018). Leveraging molecular quantitative trait loci to understand the genetic architecture of diseases and complex traits. Nature genetics, 50(7), 1041.
Liu, X., Finucane, H. K., Gusev, A., Bhatia, G., Gazal, S., O’Connor, L., ... & Price, A. L. (2017). Functional architectures of local and distal regulation of gene expression in multiple human tissues. The American Journal of Human Genetics, 100(4), 605-616.
O’Connor, L. J., & S. Feizi. Biclustering using message passing (2014). Advances in Neural Information Processing Systems, 3617-3625.