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Selected Publications

Xu, L.; Brito, I.L.; Alm, E.J.; Blainey, P.C.* Virtual microfluidics for digital quantification and single cell sequencing. (2016). Nat Methods. 2016 Aug 1. doi:10.1038/nmeth.3955. PMID: 27479330 

Brito I.L.; Yilmaz S.; Huang K.; Xu L.; Jupiter S.D.; Jenkins A.P.; Naisilisili W.; Tamminen M.; Smillie C.S.; Wortman J.R.; Birren B.W.; Xavier R.J.; Blainey P.C.*; Singh A.K.; Gevers D.; Alm E.J. Mobile genes in the human microbiome are structured from global to individual scales Nature. 2016 Jul 21;535(7612):435-9. doi: 10.1038/nature18927. PMID: 27409808 

Kim, S.; De Jonghe, J.; Vatanen, T.; Bhattacharyya, R.; Kulesa, A.; Feldman, D.; Nolan, J.; Blainey, P.C. High throughput microfluidic sample preparation for high-quality microbial isolate sequencing. (2016). In revision. No PMC.

Xiong, K.; Blainey, P.C.* Molecular sled sequences are common in mammalian proteins. Nucleic Acids Research (2016), doi: 10.1093/nar/gkw035, 1-8. PMID pending; PMC pending.

Mangel, W.F.; McGrath, W.J.; Xiong, K.; Graziano, V.; Blainey, P.C. Molecular sled: an eleven-amino acid vehicle that facilitates biochemical interactions via sliding components along DNA. Nature Communications (2015), 7, 10202, 1-11. PMID: pending; PMC: pending.

Morinishi, L.M.; Blainey, P.C. Simple bulk readout of digital nucleic acid quantification assays. J. Vis. Exp. (2015), 103, e52925. No PMID; No PMC

Kulesa, A.; Krzywinski, K.; Blainey, P.C.; Altman, N. Points of significance: sampling distributions and the bootstrap. Nature Methods (2015), 12, 477–78. PMID: 26221652; No PMC

Bennett, R. A.; Ysasi, A.B.; Belle, J.M.; Wagner, W.; Konerding; M.A.; Blainey, P.C.; Pyne, S.; Mentzer, S.J. Laser microdissection of the alveolar duct for single-cell genomic analysis. Frontiers in Oncology (2014), 4(260), 1-8. PMID: 25309876; PMC4173809

Blainey, P.C.; Quake, S. Dissecting genomic diversity, one cell at a time. Nature Methods Commentary (2014), 11, 19–21. PMID: 24524132; PMC3947563

Vestergaard, C.L.; Blainey, P.C.; Flyvbjerg, H. Optimal estimation of diffusion coefficients from single-particle trajectories. Physical Review E. Statistical, Nonlinear, and Soft Matter Physics (2014), 89(2), 022726. PMID: 25353527; No PMC

Krzywinski, K.; Altman, N.; Blainey, P.C. Points of significance: nested designs. Nature Methods (2014), 11, 977–78. PMID: 25392877; No PMC

Blainey, P.C.; Krzywinski, K.; Altman, N. Points of significance: replication. Nature Methods (2014), 11, 879–80. PMID: 25317452; No PMC

Landry, Z.C.; Giovanonni, S.J.; Quake, S.R.; Blainey, P.C. Optofluidic cell selection from complex microbial communities for single-genome analysis. Methods Enzymol (2013), 531, 61-90. PMID: 24060116; PMC3886641

Blainey, P.C. The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol Rev (2013), 37(3), 407-27. PMID: 23298390; PMC3878092

Pamp, S.J.; Harrington, E.D.; Quake, S.R.; Relman, D.A.; Blainey, P.C. Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB). Genome Research (2012), 22(6), 1107-19. PMID: 22434425; PMC3371716