[1] HodsonR. Precision medicine. Nature. 2016; 537:S49.
[2] Ashley EA. Towards precision medicine. Nature Reviews Genetics. 2016; 17: 507-522.
[3] McMurry AJ, Murphy SN, MacFadden D, Weber G, Simons WW, Orechia J, Bickel J, Wattanasin N, Gilbert C, Trevvett P, Churchill S, Kohane IS. SHRINE: Enabling nationally scalable multi-site disease studies. PLoS One. 2013; doi: 10.1371/journal.pone.0055811.
[4] Kohane IS, Churchill SE, Murphy SN. A translational engine at the national scale: informatics for integrating biology and the bedside. J Am Med Inform Assoc. 2012;19(2):181–5.
[5] Murphy SN, Weber G, Mendis M, Gainer V, Chueh HC, Churchill S, et al. Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2). J Am Med Inform Assoc. 2010;17(2):124–30.
[6] Murphy SN, Avillach P, Bellazzi R, Phillips L, Gabetta M, Eran A, McDuffie MT, Kohane IS. Combining clinical and genomics queries using i2b2 – Three methods. PLoS One. 2017; doi:10.1371/journal.pone.0172187.
[7] Datta K, Gururaj K, Naik M, Narvaez P, Rutar M. GenomicsDB: Storing Genome Data as Sparse Columnar Arrays. White Paper. Intel Health and Life Sciences; 2017.
[8] Papadopoulos, SA. The TileDB Array Data Storage Manager. Proc. VLDB Endow. 2016; 329-360.
[9] GenomicsDB [https://www.genomicsdb.org/]
[10] McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework fro analyzing next-generation DNA sequencing data. Genome Res. 2010; doi: 10.1101/gr.107524.110.
[11] Genomics Analysis Toolkit (GATK) [https://github.com/broadinstitute/gatk/]
[12] Gabetta M, Limongelli I, Rizzo E, Riva A, Segagni D, Bellazzi R. BigQ: a NoSQL based framework to handle genomic variants in i2b2. BMC Bioinformatics. 2015; doi:10.1186/s12859-015-0861-0.
[13] Zaharia M, Xin RS, Wendell P, Das T, Armbrust M, Dave A, Meng X, Rosen J, Venkataraman S, Franklin MJ, Ghodsi A, Gonzalez J, Shenker S, Stoica I. Apache Spark: a unified engine for big data processing. Communications of the ACM. 2016; doi: 10.1145/2934664.
[14] Apache Spark [https://spark.apache.org/]
[15] O’Driscoll A, Daugelaite J, Sleator RD. ‘Big data’, Hadoop and cloud computing in genomics. Journal of Biomedical Informatics. 2013; doi:10.1016/j.jbi.2013.07.001.
[16] Nothaft FA, Massie M, Danford T, Zhang Z, Laserson U, Yeksigian C, Kottalam J, Ahuja A, Hammerbacher J, Linderman M, Franklin M, Joseph AD, Patterson DA. Rethinking data-intensive science using scalable analytics systems. Proc 2015 SIGMOD. 2015.
[17] Hail [https://github.com/hail-is/hail]
[18] Zaharia M, Chowdhury M, Das T, Dave A, Ma J, McCauley M, Franklin MJ, Shenker S, Stoica I. Resilient Distributed Datasets: A fault-tolerant abstraction for in-memory cluster computing. Proc 9th USENIX Conf Network Systems Design and Impl. 2012; 2.
[19] Hadoop [http://hadoop.apache.org/]
[20] Amazon AWS EMR [https://aws.amazon.com/emr/]
[21] Amazon AWS S3 [https://aws.amazon.com/s3/]
[22] Amazon AWS [https://aws.amazon.com/]
[23] The Variant Call Format (VCF) Version 4.2 Specification. In: SAM/BAM and related specification. Samtools. 2018. https://samtools.github.io/hts-specs/VCFv4.2.pdf.
[24] Samtools HTSLib [https://github.com/samtools/htslib]
A global reference for human genetic variation, The 1000 Genomes Project Consortium, Nature 526, 68-74 (01 October 2015) doi:10.1038/nature15393.
[25] Tange O. GNU Parallel 2018. Zenodo. 2018; doi:10.5281/zenodo.1146014.
[26] PostgreSQL [https://www.postgresql.org/]
[27] Apache Zeppelin [https://zeppelin.apache.org/]
AtLAs Biobank [https://www.uclahealth.org/precision-health/atlas-california-health-initiative]
[28] MongoDB [https://www.mongodb.com/]
[29] D3.js [https://d3js.org/]
[30] i2b2 “How to”-Installation, startup and extending its functionality. In: i2b2 Informatics for Integrating Biology & the Bedside. Partners Healthcare. 2014. https://www.i2b2.org/software/tutorial.html.
[31] The 1000 Genomes Project Consortium. A global reference for human genetic variation, The 1000 Genomes Project Consortium. Nature. 2015; 526:68-74.
[32] AtLAs [https://www.uclahealth.org/precision-health/atlas-california-health-initiative]
[33] Amazon EC2 Instance Types [https://aws.amazon.com/ec2/instance-types/]