Börnigen, DanielaMoon, Yo SupRahnavard, GholamaliWaldron, LeviMcIver, LaurenShafquat, AfrahFranzosa, EricMiropolsky, LarissaSweeney, ChristopherMorgan, Xochitl C.Garrett, WendyHuttenhower, Curtis2015-08-032015Börnigen, D., Y. S. Moon, G. Rahnavard, L. Waldron, L. McIver, A. Shafquat, E. A. Franzosa, et al. 2015. “A reproducible approach to high-throughput biological data acquisition and integration.” PeerJ 3 (1): e791. doi:10.7717/peerj.791. http://dx.doi.org/10.7717/peerj.791.2167-8359http://nrs.harvard.edu/urn-3:HUL.InstRepos:17820696Modern biological research requires rapid, complex, and reproducible integration of multiple experimental results generated both internally and externally (e.g., from public repositories). Although large systematic meta-analyses are among the most effective approaches both for clinical biomarker discovery and for computational inference of biomolecular mechanisms, identifying, acquiring, and integrating relevant experimental results from multiple sources for a given study can be time-consuming and error-prone. To enable efficient and reproducible integration of diverse experimental results, we developed a novel approach for standardized acquisition and analysis of high-throughput and heterogeneous biological data. This allowed, first, novel biomolecular network reconstruction in human prostate cancer, which correctly recovered and extended the NFκB signaling pathway. Next, we investigated host-microbiome interactions. In less than an hour of analysis time, the system retrieved data and integrated six germ-free murine intestinal gene expression datasets to identify the genes most influenced by the gut microbiota, which comprised a set of immune-response and carbohydrate metabolism processes. Finally, we constructed integrated functional interaction networks to compare connectivity of peptide secretion pathways in the model organisms Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa.en-USHigh-throughput dataData integrationData acquisitionMeta-analysisHeterogeneous dataReproducibilityJournal Article2015-08-0310.7717/peerj.791