Citations

Tissue-specific networks, NetWAS

Greene CS*, Krishnan A*, Wong AK*, Ricciotti E, Zelaya RA, Himmelstein DS, Zhang R, Hartmann BM, Zaslavsky E, Sealfon SC, Chasman DI, FitzGerald GA, Dolinski K, Grosser T, Troyanskaya OG. (2015). Understanding multicellular function and disease with human tissue-specific networks. Nature Genetics. 10.1038/ng.3259.

Functional module detection

Krishnan A*, Zhang R*, Yao V, Theesfeld CL, Wong AK, Tadych A, Volfovsky N, Packer A, Lash A, Troyanskaya OG.(2016) Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder. Nature Neuroscience.

Sei

Chen, K. M., Wong, A. K., Troyanskaya, O. G., & Zhou, J. (2022), A sequence-based global map of regulatory activity for deciphering human genetics. Nature Genetics (2018).

Beluga (DeepSEA)

Beluga model: Zhou, J., Theesfeld, C. L., Yao, K., Chen, K. M., Wong, A. K., & Troyanskaya, O. G. (2018), Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk. Nature Genetics.

Original publication of the DeepSEA method: Zhou, J., & Troyanskaya, O. G. (2015) Predicting the Effects of Noncoding Variants with Deep learning-based Sequence Model Nature Methods.

Seqweaver

Park, C. Y., Zhou, J., Wong, A. K., Chen, K. M., Theesfeld, C. L., Darnell, R. B., & Troyanskaya, O. G. (2021). Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk. Nat Genet.

ExPecto

Zhou, J., Theesfeld, C. L., Yao, K., Chen, K. M., Wong, A. K., & Troyanskaya, O. G. (2018), Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk, Nature Genetics.

ExPectoSC

Sokolova, K., Theesfeld, C. L., Wong, A. K., Zhang, Z., Dolinski, K., & Troyanskaya, O. G. (2023), Atlas of primary cell-type specific sequence models of gene expression and variant effects. Cell Reports Methods.

Autism variant effect predictions

Zhou, J.*, Park, C. Y.*, Theesfeld, C. L.*, Wong, A. K., Yuan, Y., Scheckel, C., … & Troyanskaya, O. G. (2019). Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk. Nature genetics, 51(6), 973-980.

Tissue-expression predictions

Ju, W.*, Greene, C. S.8, Eichinger, F., Nair, V., Hodgin, J. B., Bitzer, M., … Troyanskaya, O. G.* & Kretzler, M*. (2013). Defining cell-type specificity at the transcriptional level in human disease. Genome Research.