More info on my Google Scholar profile


  • Donoghue T, Voytek B, and Ellis SE (2020). Teaching Creative and Practical Data Science at Scale. Journal of Statistics Education [link]


  • Madugundu AK, Hyun Na C, Nirujogi RS, Reunuse S, Kim KP, Burns KH, Langmead B, Ellis SE, Collado-Torres L, Halushka MK, Kim M, Pandey A (2019) Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial cells. Proteomics. [link]


  • Ellis SE, Collado-Torres L, Jaffe AE, Leek JT (2018) Improving the value of public RNA-seq expression data by phenotype prediction. Nucleic Acids Research. [link]


  • Andrews SV, Ellis SE, Bakulski KM, Sheppard B, Croen LA, Hertz-Picciotto I, Newschaffer CJ, Feinberg AP, Arking DE, Ladd-Acosta C, Fallin MD (2017) Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder. Nature Communications. [link]

  • Ellis SE and Leek JT (2017) How to share data for collaboration. The American Statistician. [link]

  • Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA Hansen KD, Jaffe AE, Langmead B, Leek JT (2017) Reproducible RNA-seq analysis using recount2. Nature Biotechnology doi: 10.1038/nbt.3838 [link] [database] [reproducible analysis] [software]

  • Ellis SE, Gupta S, Moes A, West AB, Arking DE (2017) Exaggerated CpH Methylation in the Autism-Affected Brain. Molecular Autism doi: 10.1186/s13229-017-0119-y [link]


  • Ellis SE, Panitch R, West AB, Arking DE (2016) Transcriptome analysis of cortical tissue reveals shared sets of downregulated genes in autism and schizophrenia. Translational Psychiatry doi: 10.1038/tp.2016.87 [link]


  • Huang, Haritunas, Okou, et al. (2015) Characterization of genetic loci that affect susceptibility to inflammatory bowel diseases in African Americans. Gastroenterolgy doi: 10.1053/j.gastro.2015.07.065 [link]


  • Gupta S, Ellis SE, Ashar FN, Moes A, Baser JS, Zhan J, West AB, Arking DE (2014) Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism. Nature Communications doi: doi:10.1038/ncomms6748 [link]


  • Ellis SE, Gupta S, Ashar FN, Bader JS, West AB, Arking DE. (2013) RNA-Seq optimization with eQTL gold standards. BMC Genomics doi: 10.11861471-2164-14-892 [link]