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Citations
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Tissue-specific networks, NetWAS
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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 <http://www.nature.com/ng/journal/v47/n6/full/ng.3259.html>`_. Nature Genetics. 10.1038/ng.3259.

Functional module detection
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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 <https://www.nature.com/articles/nn.4353>`_. Nature Neuroscience.

Sei
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Chen, K. M., Wong, A. K., Troyanskaya, O. G., & Zhou, J. (2022), `A sequence-based global map of regulatory activity for deciphering human genetics <https://www.nature.com/articles/s41588-022-01102-2>`_. Nature Genetics (2018).

Beluga (DeepSEA)
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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 <https://www.nature.com/articles/s41588-018-0160-6>`_. 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 <https://www.nature.com/articles/nmeth.3547>`_ Nature Methods.

Seqweaver
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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 <https://www.nature.com/articles/s41588-020-00761-3>`_. Nat Genet.


ExPecto
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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 <https://www.nature.com/articles/s41588-018-0160-6>`_, Nature Genetics.

ExPectoSC
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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 <https://www.cell.com/cell-reports-methods/fulltext/S2667-2375(23)00224-2>`_. Cell Reports Methods.

Autism variant effect predictions
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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 <https://www.nature.com/articles/s41588-019-0420-0>`_. Nature genetics, 51(6), 973-980.

Tissue-expression predictions
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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 <https://genome.cshlp.org/content/23/11/1862.full.pdf>`_. Genome Research.