Preprints
2019
79. Gazestani, V.H., Pramparo, T., Nalabolu, S., Kellman, B.P., Murray, S., Lopez, L., Pierce, K., Courchesne, E., Lewis, N.E. Transcriptional organization of autism spectrum disorder and its connection to ASD risk genes and phenotypic variation. Nature Neuroscience, accepted (2019). bioRxiv: 10.1101/435917
75. Gazestani, V.H., Lewis, N.E. From Genotype to Phenotype: Augmenting Deep Learning with Networks and Systems Biology, Current Opinion in Systems Biology, 15:68-73 (2019). DOI: 10.1016/j.coisb.2019.04.001
2018
66. Lombardo, M.V., Pramparo, T., Gazestani, V., Warrier, V., Bethlehem, R.AI., Barnes, C.C., Lopez, L., Lewis, N.E., Eyler, L., Pierce, K., Courchesne, E. Large-scale associations between the leukocyte transcriptome and BOLD responses to speech differ in autism early language outcome subtypes, Nature Neuroscience, 21, 1680–1688 (2018). DOI: 10.1038/s41593-018-0281-3
59. Courchesne, E., Pramparo, T., Gazestani, V.H., Lombardo, M.V., Pierce, K., Lewis, N.E. (2018) The ASD living biology: From cell proliferation to clinical phenotype. Molecular Psychiatry, 24:88-107. DOI: 10.1038/s41380-018-0056-y
2017
47. Lombardo, M.V., Courchesne, E., Lewis, N.E., Pramparo, T. Hierarchical cortical transcriptome disorganization in autism. Molecular Autism, 8:29 (2017). DOI: 10.1186/s13229-017-0147-7
2015
38. Pramparo, T., Campbell, K., Barnes, C.C., Marinero, S., Solso, S., Young, J., Mayo, M., Dale, A., Ahrens-Barbeau, C., Murray, S.S., Lopez, L., Lewis, N.E., Pierce, K., Courchesne, E. Cell Cycle Networks link Gene Expression Dysregulation, Mutation and Brain Maldevelopment in Autistic Toddlers. Molecular Systems Biology, 11: 841 (2015). DOI:10.15252/msb.20156108
2014
30. Busskamp, V.*, Lewis, N.E.*, Guye, P.*, Ng, A.H.M., Shipman, S.L., Byrne, S.M., Sanjana, N.E., Murn, J., Li, Y., Li, S., Stadler, M., Weiss, R., Church, G.M. Rapid neurogenesis through transcriptional activation in human stem cells. Molecular Systems Biology, 10:760 (2014). DOI: 10.15252/msb.20145508. * equal contribution
2010
9. Lewis, N.E., Schramm, G., Bordbar, A., Schellenberger, J., Andersen, M.P., Cheng, J.K., Patel, N., Yee, A., Lewis, R.A., Eils, R., König, R., Palsson, B.Ø. Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nature Biotechnology, 28:1279–1285 (2010). Paper highlighted by Nature Methods (January 2011).
Patents and patent applications
4. Lewis, N.E., Gazestani, V., Pramparo, T., Courchesne, E. Expression-based diagnosis, prognosis, and treatment of complex diseases. Patent pending – provisional.
