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Paul C. Blainey, Ph.D. - Publications

Affiliations: 
2007 Harvard University, Cambridge, MA, United States 
Area:
room-temperature single-molecule spectroscopy
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38 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Banal JL, Shepherd TR, Berleant J, Huang H, Reyes M, Ackerman CM, Blainey PC, Bathe M. Random access DNA memory using Boolean search in an archival file storage system. Nature Materials. PMID 34112975 DOI: 10.1038/s41563-021-01021-3  0.318
2021 Elacqua JJ, Ranu N, DiIorio SE, Blainey PC. DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution. Genome Research. 31: 75-87. PMID 33355294 DOI: 10.1101/gr.265223.120  0.33
2021 Elacqua JJ, Ranu N, DiIorio SE, Blainey PC. DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution. Genome Research. 31: 75-87. PMID 33355294 DOI: 10.1101/gr.265223.120  0.33
2019 Schmidt ST, Yu FB, Blainey PC, May AP, Quake SR. Nucleic acid cleavage with a hyperthermophilic Cas9 from an uncultured Ignavibacterium. Proceedings of the National Academy of Sciences of the United States of America. PMID 31659048 DOI: 10.1073/Pnas.1904273116  0.337
2018 Brody Y, Kimmerling RJ, Maruvka YE, Benjamin D, Elacqua JJ, Haradhvala NJ, Kim J, Mouw KW, Frangaj K, Koren A, Getz G, Manalis SR, Blainey PC. Quantification of somatic mutation flow across individual cell division events by lineage sequencing. Genome Research. PMID 30459213 DOI: 10.1101/Gr.238543.118  0.353
2018 Ranu N, Villani AC, Hacohen N, Blainey PC. Targeting individual cells by barcode in pooled sequence libraries. Nucleic Acids Research. PMID 30256981 DOI: 10.1093/Nar/Gky856  0.337
2018 Landry ZC, Vergin K, Mannenbach C, Block S, Yang Q, Blainey P, Carlson C, Giovannoni S. Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface. Frontiers in Microbiology. 9: 1152. PMID 29937754 DOI: 10.3389/Fmicb.2018.01152  0.301
2018 Vestergaard CL, Blainey PC, Flyvbjerg H. Single-particle trajectories reveal two-state diffusion-kinetics of hOGG1 proteins on DNA. Nucleic Acids Research. PMID 29361033 DOI: 10.1093/Nar/Gky004  0.355
2017 Xiong K, Blainey PC. A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA. Journal of Visualized Experiments : Jove. PMID 28994817 DOI: 10.3791/55923  0.429
2017 Yu FB, Blainey PC, Schulz F, Woyke T, Horowitz MA, Quake SR. Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples. Elife. 6. PMID 28678007 DOI: 10.7554/Elife.26580  0.314
2017 Kim S, De Jonghe J, Kulesa AB, Feldman D, Vatanen T, Bhattacharyya RP, Berdy B, Gomez J, Nolan J, Epstein S, Blainey PC. High-throughput automated microfluidic sample preparation for accurate microbial genomics. Nature Communications. 8: 13919. PMID 28128213 DOI: 10.1038/Ncomms13919  0.362
2016 Xiong K, Erwin GS, Ansari AZ, Blainey PC. Sliding on DNA: From Peptides to Small Molecules. Angewandte Chemie (International Ed. in English). PMID 27813331 DOI: 10.1002/Anie.201606768  0.477
2016 Xu L, Brito IL, Alm EJ, Blainey PC. Virtual microfluidics for digital quantification and single-cell sequencing. Nature Methods. PMID 27479330 DOI: 10.1038/Nmeth.3955  0.381
2016 Xiong K, Blainey PC. Molecular sled sequences are common in mammalian proteins. Nucleic Acids Research. PMID 26857546 DOI: 10.1093/Nar/Gkw035  0.434
2016 Mangel WF, McGrath WJ, Xiong K, Graziano V, Blainey PC. Molecular sled is an eleven-amino acid vehicle facilitating biochemical interactions via sliding components along DNA. Nature Communications. 7: 10202. PMID 26831565 DOI: 10.1038/Ncomms10202  0.459
2015 Morinishi LS, Blainey P. Simple Bulk Readout of Digital Nucleic Acid Quantification Assays. Journal of Visualized Experiments : Jove. PMID 26436576 DOI: 10.3791/52925  0.328
2015 Guo S, Veneziano R, McConnell RE, Agasti S, Gordonov S, Kulesa T, Gertler FB, Blainey P, Boyden E, Yin P, Bathe M. Quantitative Multiplexed Super-Resolution Neuronal Synapse Imaging using DNA-Paint Biophysical Journal. 108: 477a. DOI: 10.1016/J.Bpj.2014.11.2609  0.35
2014 Vestergaard CL, Blainey PC, Flyvbjerg H. Optimal estimation of diffusion coefficients from single-particle trajectories. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 89: 022726. PMID 25353527 DOI: 10.1103/Physreve.89.022726  0.319
2013 Landry ZC, Giovanonni SJ, Quake SR, Blainey PC. Optofluidic cell selection from complex microbial communities for single-genome analysis Methods in Enzymology. 531: 61-90. PMID 24060116 DOI: 10.1016/B978-0-12-407863-5.00004-6  0.312
2013 Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, Ross CA, Tringe SG, Chain PS, Scholz MB, Lo CC, Raymond J, Quake SR, Hedlund BP. Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nature Communications. 4: 1854. PMID 23673639 DOI: 10.1038/Ncomms2884  0.318
2013 Blainey PC. The future is now: single-cell genomics of bacteria and archaea. Fems Microbiology Reviews. 37: 407-27. PMID 23298390 DOI: 10.1111/1574-6976.12015  0.321
2013 Blainey PC, Graziano V, Pérez-Berná AJ, McGrath WJ, Flint SJ, San Martín C, Xie XS, Mangel WF. Regulation of a viral proteinase by a peptide and DNA in one-dimensional space: IV. viral proteinase slides along DNA to locate and process its substrates. The Journal of Biological Chemistry. 288: 2092-102. PMID 23043138 DOI: 10.1074/Jbc.M112.407460  0.575
2013 Graziano V, Luo G, Blainey PC, Pérez-Berná AJ, McGrath WJ, Flint SJ, San Martín C, Xie XS, Mangel WF. Regulation of a viral proteinase by a peptide and DNA in one-dimensional space: II. adenovirus proteinase is activated in an unusual one-dimensional biochemical reaction. The Journal of Biological Chemistry. 288: 2068-80. PMID 23043137 DOI: 10.1074/Jbc.M112.407312  0.667
2013 Graziano V, McGrath WJ, Suomalainen M, Greber UF, Freimuth P, Blainey PC, Luo G, Xie XS, Mangel WF. Regulation of a viral proteinase by a peptide and DNA in one-dimensional space: I. binding to DNA AND to hexon of the precursor to protein VI, pVI, of human adenovirus. The Journal of Biological Chemistry. 288: 2059-67. PMID 23043136 DOI: 10.1074/Jbc.M112.377150  0.657
2012 Marshall IPG, Blainey PC, Spormann AM, Quake SR. A single-cell genome for Thiovulum sp. Applied and Environmental Microbiology. 78: 8555-8563. PMID 23023751 DOI: 10.1128/Aem.02314-12  0.318
2012 Pamp SJ, Harrington ED, Quake SR, Relman DA, Blainey PC. Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB). Genome Research. 22: 1107-19. PMID 22434425 DOI: 10.1101/Gr.131482.111  0.319
2011 Kalisky T, Blainey P, Quake SR. Genomic analysis at the single-cell level Annual Review of Genetics. 45: 431-445. PMID 21942365 DOI: 10.1146/Annurev-Genet-102209-163607  0.301
2011 Youssef NH, Blainey PC, Quake SR, Elshahed MS. Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone spring, Oklahoma) Applied and Environmental Microbiology. 77: 7804-7814. PMID 21908640 DOI: 10.1128/Aem.06059-11  0.314
2011 Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR. Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. Plos One. 6: e16626. PMID 21364937 DOI: 10.1371/Journal.Pone.0016626  0.347
2011 Blainey PC, Quake SR. Digital MDA for enumeration of total nucleic acid contamination Nucleic Acids Research. 39: e19. PMID 21071419 DOI: 10.1093/Nar/Gkq1074  0.434
2010 Vestergaard CL, Blainey P, Xie XS, Flyvbjerg H. Optimal Estimation of the Diffusion Coefficient from Noisy Time-Series Measurements Biophysical Journal. 98: 188a. DOI: 10.1016/J.Bpj.2009.12.1005  0.485
2009 Blainey PC, Luo G, Kou SC, Mangel WF, Verdine GL, Bagchi B, Xie XS. Nonspecifically bound proteins spin while diffusing along DNA. Nature Structural & Molecular Biology. 16: 1224-9. PMID 19898474 DOI: 10.1038/Nsmb.1716  0.66
2009 White RA, Blainey PC, Fan HC, Quake SR. Digital PCR provides sensitive and absolute calibration for high throughput sequencing. Bmc Genomics. 10: 116. PMID 19298667 DOI: 10.1186/1471-2164-10-116  0.353
2008 Bagchi B, Blainey PC, Xie XS. Diffusion constant of a nonspecifically bound protein undergoing curvilinear motion along DNA. The Journal of Physical Chemistry. B. 112: 6282-4. PMID 18321088 DOI: 10.1021/Jp077568F  0.553
2007 Kim S, Blainey PC, Schroeder CM, Xie XS. Multiplexed single-molecule assay for enzymatic activity on flow-stretched DNA. Nature Methods. 4: 397-9. PMID 17435763 DOI: 10.1038/Nmeth1037  0.683
2006 Blainey PC, van Oijen AM, Banerjee A, Verdine GL, Xie XS. A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proceedings of the National Academy of Sciences of the United States of America. 103: 5752-7. PMID 16585517 DOI: 10.1073/Pnas.0509723103  0.676
2005 Schroeder CM, Kim S, Blainey PC, Xie XS. Single molecule kinetics of reverse transcriptase Aiche Annual Meeting, Conference Proceedings. 8076.  0.462
2003 van Oijen AM, Blainey PC, Crampton DJ, Richardson CC, Ellenberger T, Xie XS. Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder. Science (New York, N.Y.). 301: 1235-8. PMID 12947199 DOI: 10.1126/Science.1084387  0.674
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