Erika Bongen

All Publications

• EMPOWERING MULTI-COHORT GENE EXPRESSION ANALYSIS TO INCREASE REPRODUCIBILITY. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Haynes, W. A., Vallania, F., Liu, C., Bongen, E., Tomczak, A., Andres-Terrè, M., Lofgren, S., Tam, A., Deisseroth, C. A., Li, M. D., Sweeney, T. E., Khatri, P. 2016; 22: 144-153

  Abstract

  A major contributor to the scientific reproducibility crisis has been that the results from homogeneous, single-center studies do not generalize to heterogeneous, real world populations. Multi-cohort gene expression analysis has helped to increase reproducibility by aggregating data from diverse populations into a single analysis. To make the multi-cohort analysis process more feasible, we have assembled an analysis pipeline which implements rigorously studied meta-analysis best practices. We have compiled and made publicly available the results of our own multi-cohort gene expression analysis of 103 diseases, spanning 615 studies and 36,915 samples, through a novel and interactive web application. As a result, we have made both the process of and the results from multi-cohort gene expression analysis more approachable for non-technical users.

  View details for PubMedID 27896970

  View details for PubMedCentralID PMC5167529

• Integrated, Multi-cohort Analysis Identifies Conserved Transcriptional Signatures across Multiple Respiratory Viruses IMMUNITY Andres-Terre, M., McGuire, H. M., Pouliot, Y., Bongen, E., Sweeney, T. E., Tato, C. M., Khatri, P. 2015; 43 (6): 1199-1211

  Abstract

  Respiratory viral infections are a significant burden to healthcare worldwide. Many whole genome expression profiles have identified different respiratory viral infection signatures, but these have not translated to clinical practice. Here, we performed two integrated, multi-cohort analyses of publicly available transcriptional data of viral infections. First, we identified a common host signature across different respiratory viral infections that could distinguish (1) individuals with viral infections from healthy controls and from those with bacterial infections, and (2) symptomatic from asymptomatic subjects prior to symptom onset in challenge studies. Second, we identified an influenza-specific host response signature that (1) could distinguish influenza-infected samples from those with bacterial and other respiratory viral infections, (2) was a diagnostic and prognostic marker in influenza-pneumonia patients and influenza challenge studies, and (3) was predictive of response to influenza vaccine. Our results have applications in the diagnosis, prognosis, and identification of drug targets in viral infections.

  View details for DOI 10.1016/j.immuni.2015.11.003

  View details for Web of Science ID 000366846600022

  View details for PubMedID 26682989

  View details for PubMedCentralID PMC4684904