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Items: 42

1.

Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens.

Berghuis BA, Yu FB, Schulz F, Blainey PC, Woyke T, Quake SR.

Proc Natl Acad Sci U S A. 2019 Mar 12;116(11):5037-5044. doi: 10.1073/pnas.1815631116. Epub 2019 Feb 27.

2.

Multiplexed enrichment and genomic profiling of peripheral blood cells reveal subset-specific immune signatures.

Reyes M, Vickers D, Billman K, Eisenhaure T, Hoover P, Browne EP, Rao DA, Hacohen N, Blainey PC.

Sci Adv. 2019 Jan 23;5(1):eaau9223. doi: 10.1126/sciadv.aau9223. eCollection 2019 Jan.

3.

Commensal Microbiota Promote Lung Cancer Development via γδ T Cells.

Jin C, Lagoudas GK, Zhao C, Bullman S, Bhutkar A, Hu B, Ameh S, Sandel D, Liang XS, Mazzilli S, Whary MT, Meyerson M, Germain R, Blainey PC, Fox JG, Jacks T.

Cell. 2019 Feb 21;176(5):998-1013.e16. doi: 10.1016/j.cell.2018.12.040. Epub 2019 Jan 31.

PMID:
30712876
4.

Quantification of somatic mutation flow across individual cell division events by lineage sequencing.

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.

Genome Res. 2018 Dec;28(12):1901-1918. doi: 10.1101/gr.238543.118. Epub 2018 Nov 20.

5.

Targeting individual cells by barcode in pooled sequence libraries.

Ranu N, Villani AC, Hacohen N, Blainey PC.

Nucleic Acids Res. 2019 Jan 10;47(1):e4. doi: 10.1093/nar/gky856.

6.

Combinatorial drug discovery in nanoliter droplets.

Kulesa A, Kehe J, Hurtado JE, Tawde P, Blainey PC.

Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):6685-6690. doi: 10.1073/pnas.1802233115. Epub 2018 Jun 13.

7.

Single-particle trajectories reveal two-state diffusion-kinetics of hOGG1 proteins on DNA.

Vestergaard CL, Blainey PC, Flyvbjerg H.

Nucleic Acids Res. 2018 Mar 16;46(5):2446-2458. doi: 10.1093/nar/gky004.

8.

Trends in Antibiotic Susceptibility in Staphylococcus aureus in Boston, Massachusetts, from 2000 to 2014.

Kanjilal S, Sater MRA, Thayer M, Lagoudas GK, Kim S, Blainey PC, Grad YH.

J Clin Microbiol. 2017 Dec 26;56(1). pii: e01160-17. doi: 10.1128/JCM.01160-17. Print 2018 Jan.

10.

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples.

Yu FB, Blainey PC, Schulz F, Woyke T, Horowitz MA, Quake SR.

Elife. 2017 Jul 5;6. pii: e26580. doi: 10.7554/eLife.26580.

11.

Corrigendum: Mobile genes in the human microbiome are structured from global to individual scales.

Brito IL, Yilmaz S, Huang K, Xu L, Jupiter SD, Jenkins AP, Naisilisili W, Tamminen M, Smillie CS, Wortman JR, Birren BW, Xavier RJ, Blainey PC, Singh AK, Gevers D, Alm EJ.

Nature. 2017 Apr 6;544(7648):124. doi: 10.1038/nature20774. Epub 2017 Mar 22. No abstract available.

PMID:
28329759
12.

High-throughput automated microfluidic sample preparation for accurate microbial genomics.

Kim S, De Jonghe J, Kulesa AB, Feldman D, Vatanen T, Bhattacharyya RP, Berdy B, Gomez J, Nolan J, Epstein S, Blainey PC.

Nat Commun. 2017 Jan 27;8:13919. doi: 10.1038/ncomms13919.

13.

Sliding on DNA: From Peptides to Small Molecules.

Xiong K, Erwin GS, Ansari AZ, Blainey PC.

Angew Chem Int Ed Engl. 2016 Nov 21;55(48):15110-15114. doi: 10.1002/anie.201606768. Epub 2016 Nov 4.

14.

Funding: Interdisciplinary challenges.

Blainey PC.

Nat Microbiol. 2016 Jul 26;1(8):16118. doi: 10.1038/nmicrobiol.2016.118. No abstract available.

PMID:
27573117
15.

Virtual microfluidics for digital quantification and single-cell sequencing.

Xu L, Brito IL, Alm EJ, Blainey PC.

Nat Methods. 2016 Sep;13(9):759-62. doi: 10.1038/nmeth.3955. Epub 2016 Aug 1.

16.

Mobile genes in the human microbiome are structured from global to individual scales.

Brito IL, Yilmaz S, Huang K, Xu L, Jupiter SD, Jenkins AP, Naisilisili W, Tamminen M, Smillie CS, Wortman JR, Birren BW, Xavier RJ, Blainey PC, Singh AK, Gevers D, Alm EJ.

Nature. 2016 Jul 21;535(7612):435-439. doi: 10.1038/nature18927. Epub 2016 Jul 13. Erratum in: Nature. 2017 Apr 6;544(7648):124.

17.

Molecular sled sequences are common in mammalian proteins.

Xiong K, Blainey PC.

Nucleic Acids Res. 2016 Mar 18;44(5):2266-73. doi: 10.1093/nar/gkw035. Epub 2016 Feb 8.

18.

Molecular sled is an eleven-amino acid vehicle facilitating biochemical interactions via sliding components along DNA.

Mangel WF, McGrath WJ, Xiong K, Graziano V, Blainey PC.

Nat Commun. 2016 Feb 2;7:10202. doi: 10.1038/ncomms10202.

19.

A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages.

Kimmerling RJ, Lee Szeto G, Li JW, Genshaft AS, Kazer SW, Payer KR, de Riba Borrajo J, Blainey PC, Irvine DJ, Shalek AK, Manalis SR.

Nat Commun. 2016 Jan 6;7:10220. doi: 10.1038/ncomms10220.

20.

Tools for the Microbiome: Nano and Beyond.

Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Fraser SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GC, Wright AT, Young TD.

ACS Nano. 2016 Jan 26;10(1):6-37. doi: 10.1021/acsnano.5b07826. Epub 2015 Dec 22. Review.

PMID:
26695070
21.

Optimal estimation of diffusion coefficients from single-particle trajectories.

Vestergaard CL, Blainey PC, Flyvbjerg H.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Feb;89(2):022726. Epub 2014 Feb 28.

PMID:
25353527
22.

Laser microdissection of the alveolar duct enables single-cell genomic analysis.

Bennett RD, Ysasi AB, Belle JM, Wagner WL, Konerding MA, Blainey PC, Pyne S, Mentzer SJ.

Front Oncol. 2014 Sep 24;4:260. doi: 10.3389/fonc.2014.00260. eCollection 2014.

23.

Dissecting genomic diversity, one cell at a time.

Blainey PC, Quake SR.

Nat Methods. 2014 Jan;11(1):19-21. No abstract available. Erratum in: Nat Methods. 2014 Mar;11(3):349.

24.

Optofluidic cell selection from complex microbial communities for single-genome analysis.

Landry ZC, Giovanonni SJ, Quake SR, Blainey PC.

Methods Enzymol. 2013;531:61-90. doi: 10.1016/B978-0-12-407863-5.00004-6.

25.

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage.

Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, Ross CA, Tringe SG, Chain PS, Scholz MB, Lo CC, Raymond J, Quake SR, Hedlund BP.

Nat Commun. 2013;4:1854. doi: 10.1038/ncomms2884.

26.

The future is now: single-cell genomics of bacteria and archaea.

Blainey PC.

FEMS Microbiol Rev. 2013 May;37(3):407-27. doi: 10.1111/1574-6976.12015. Epub 2013 Feb 11. Review.

27.

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.

Blainey PC, Graziano V, Pérez-Berná AJ, McGrath WJ, Flint SJ, San Martín C, Xie XS, Mangel WF.

J Biol Chem. 2013 Jan 18;288(3):2092-102. doi: 10.1074/jbc.M112.407460. Epub 2012 Oct 7.

28.

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.

Graziano V, Luo G, Blainey PC, Pérez-Berná AJ, McGrath WJ, Flint SJ, San Martín C, Xie XS, Mangel WF.

J Biol Chem. 2013 Jan 18;288(3):2068-80. doi: 10.1074/jbc.M112.407312. Epub 2012 Oct 7.

29.

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.

Graziano V, McGrath WJ, Suomalainen M, Greber UF, Freimuth P, Blainey PC, Luo G, Xie XS, Mangel WF.

J Biol Chem. 2013 Jan 18;288(3):2059-67. doi: 10.1074/jbc.M112.377150. Epub 2012 Oct 7.

30.

A Single-cell genome for Thiovulum sp.

Marshall IP, Blainey PC, Spormann AM, Quake SR.

Appl Environ Microbiol. 2012 Dec;78(24):8555-63. doi: 10.1128/AEM.02314-12. Epub 2012 Sep 28.

31.

Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis.

Blainey PC, Milla CE, Cornfield DN, Quake SR.

Sci Transl Med. 2012 Sep 26;4(153):153ra130.

32.

Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB).

Pamp SJ, Harrington ED, Quake SR, Relman DA, Blainey PC.

Genome Res. 2012 Jun;22(6):1107-19. doi: 10.1101/gr.131482.111. Epub 2012 Mar 20.

33.

Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma).

Youssef NH, Blainey PC, Quake SR, Elshahed MS.

Appl Environ Microbiol. 2011 Nov;77(21):7804-14. doi: 10.1128/AEM.06059-11. Epub 2011 Sep 9.

34.

Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis.

Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR.

PLoS One. 2011 Feb 22;6(2):e16626. doi: 10.1371/journal.pone.0016626.

35.

Digital MDA for enumeration of total nucleic acid contamination.

Blainey PC, Quake SR.

Nucleic Acids Res. 2011 Mar;39(4):e19. doi: 10.1093/nar/gkq1074. Epub 2010 Nov 11.

36.

Nonspecifically bound proteins spin while diffusing along DNA.

Blainey PC, Luo G, Kou SC, Mangel WF, Verdine GL, Bagchi B, Xie XS.

Nat Struct Mol Biol. 2009 Dec;16(12):1224-9. doi: 10.1038/nsmb.1716. Epub 2009 Nov 8.

37.

Digital PCR provides sensitive and absolute calibration for high throughput sequencing.

White RA 3rd, Blainey PC, Fan HC, Quake SR.

BMC Genomics. 2009 Mar 19;10:116. doi: 10.1186/1471-2164-10-116. Erratum in: BMC Genomics. 2009;10:541.

38.

Diffusion constant of a nonspecifically bound protein undergoing curvilinear motion along DNA.

Bagchi B, Blainey PC, Xie XS.

J Phys Chem B. 2008 May 15;112(19):6282-4. doi: 10.1021/jp077568f. Epub 2008 Mar 6.

PMID:
18321088
39.

Multiplexed single-molecule assay for enzymatic activity on flow-stretched DNA.

Kim S, Blainey PC, Schroeder CM, Xie XS.

Nat Methods. 2007 May;4(5):397-9. Epub 2007 Apr 15.

PMID:
17435763
40.

A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA.

Blainey PC, van Oijen AM, Banerjee A, Verdine GL, Xie XS.

Proc Natl Acad Sci U S A. 2006 Apr 11;103(15):5752-7. Epub 2006 Apr 3.

41.

Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder.

van Oijen AM, Blainey PC, Crampton DJ, Richardson CC, Ellenberger T, Xie XS.

Science. 2003 Aug 29;301(5637):1235-8.

42.

FTIR studies of intermolecular hydrogen bonding in halogenated ethanols.

Blainey PC, Reid PJ.

Spectrochim Acta A Mol Biomol Spectrosc. 2001 Dec;57(14):2763-74.

PMID:
11789877

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