Publications

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See below for our recent publications in peer-reviewed journals, books, and patents. Also, icons to the right filter publications by major topics. Public presentations and lectures can also be downloaded from here.

corresponding/senior author, * equal contribution
For a current list, click here.

Preprints

143. Bao B., Gazestani V.H., Xiao Y., Kim R., Chiang A.W.T., Nalabolu S., Pierce K., Robasky K., Lewis N.E.‡, Courchesne, E.‡. A Highly Accurate Ensemble Classifier for the Molecular Diagnosis of ASD at Ages 1 to 4 Years. medRxiv (2021). doi: 10.1101/2021.07.08.21260225

142. Chiang A.W.T., Gazestani V.H., Altieri M.G., Courchesne E., Lewis N.E. Optimal balancing of clinical factors in large scale clinical RNA-Seq studies. bioRxiv (2021). doi: 10.1101/2021.06.30.450639

141. Robasky K., Kim R., Yi H., Xu H., Bao B., Chiang A.W.T., Courchesne E., Lewis N.E. Transfer learning improves outcome predictions for ASD from gene expression in blood. bioRxiv (2021). doi: 10.1101/2021.06.26.449864

134. Gazestani, V., Chiang, A.W.T., Courchesne, E.‡, Lewis, N.E. Autism genetics perturb prenatal neurodevelopment through a hierarchy of broadly-expressed and brain-specific genes. bioRxiv (2020). DOI: 10.1101/2020.05.24.112623

2022

130. Xiao Y, Wen TH, Kupis L, Eyler L, Goel D, Vaux K, Lombardo MV, Lewis NE, Pierce K, Courchesne E. Neural responses to affective speech, including motherese, map onto clinical and social eye tracking profiles in ASD toddlers. Nature Human Behavior, in press (2022).

2021

123. Lombardo MV, Eyler L, Pramparo T, Gazestani VH, Hagler Jr. DJ, Chen CH, Dale AM, Seidlitz J, Bethlehem RAI, Bertelsen N, Barnes CC, Lopez L, Campbell K, Lewis NE, Pierce K, Courchesne E. Atypical genomic patterning of the cerebral cortex in autism with poor early language outcome, Science Advances, 7: eabh1663 (2021). DOI:10.1126/sciadv.abh1663

120. Kuo, C.C., Chiang, A.W.T., Baghdassarian H.M., Lewis, N.E. Dysregulation of the secretory pathway connects Alzheimer’s disease genetics to aggregate formation. Cell Systems, 12: P873-884.E4, (2021). DOI: 10.1016/j.cels.2021.06.001 bioRxiv DOI: 10.1101/2020.08.10.243634, PMCID: PMC8505362. Highlighted by ScienceNews.dk

119. Richelle, A., Kellman, B.P., Wenzel, A.T., Chiang, A.W.T., Reagan, T., Gutierrez, J.M., Joshi, C., Li, S., Liu, J.K., Masson, H., Lee, J., Li, Z., Heirendt, L., Trefois, C., Juarez, E.F., Bath, T., Borland, D., Mesirov, J.P., Robasky, K., Lewis, N.E. Model-based assessment of mammalian cells metabolic functionalities from omics data. Cell Reports Methods, 1:100040 (2021). DOI: 10.1016/j.crmeth.2021.100040

107. Kellman, B.P.*, Baghdassarian, H.M.*,Pramparo, T., Shamie, I., Gazestani, V.H., Begzati, A., Li, S., Nalabolu, S., Murray, S., Lopez, L., Pierce, K., Courchesne, E., Lewis, N.E. Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing. BMC Genomics, 22, 69 (2021). DOI: 10.1186/s12864-021-07381-z, PMCID: PMC7818915

2020

92. Courchesne, E.*, Gazestani, V.H.*, Lewis, N.E.* Prenatal origins of ASD: The when, what and how of ASD development. Trends in Neurosciences, 43:326 (2020).

2019

85. Gazestani, V.H., Pramparo, T., Nalabolu, S., Kellman, B.P., Murray, S., Lopez, L., Pierce, K., Courchesne, E., Lewis, N.E. A perturbed gene network containing PI3K/AKT, RAS/ERK, WNT/β-catenin pathways in leukocytes is linked to ASD genetics and symptom severityNature Neuroscience, 22, 1624–1634 (2019). DOI: 10.1038/s41593-019-0489-x, bioRxiv: 10.1101/435917, News coverage: Spectrum News, Genomeweb, Medical News, Technology Networks, Neuroscience News

2018

67. 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 subtypesNature Neuroscience, 21, 1680–1688 (2018). DOI: 10.1038/s41593-018-0281-3 News Coverage: ScienceNews.dk

60. 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 phenotypeMolecular 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 autismMolecular Autism, 8:29 (2017). DOI: 10.1186/s13229-017-0147-7

2016

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 ToddlersMolecular 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 cellsMolecular Systems Biology, 10:760 (2014). DOI: 10.15252/msb.20145508. * equal contribution

2013

2012

2011

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 brainNature Biotechnology, 28:1279–1285 (2010). Paper highlighted by Nature Methods (January 2011).

2009

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2004

Patents and applications

4. Lewis, N.E., Gazestani, V., Pramparo, T., Courchesne, E. Expression-based diagnosis, prognosis, and treatment of complex diseases. Patent PCT/US2019/041618.