Publications
2009
- J. P. C. da Cunhaa, P. A. F. Galantea, J. E. de Souzaa, R. F. de Souzaa, P. M. Carvalhoa, D. T. Oharaa, R. P. Mouraa, S. M. Oba-Shinjab, S. K. N. Marieb, W. A. Silva, Jr.c, R. O. Perezd, B. Stranskye, M. Pieprzykf, J. Mooref, O. Caballerog, J. Gama-Rodriguesd, A. Habr-Gamad, W. P. Kuoh, A. J. Simpsong, A. A. Camargoa, Lloyd J. Oldg, S. J. de Souzaa 2009 Sept 15. Bioinformatics construction of the human cell surfaceome
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- Pushkarev, D., Neff, N.F., Quake, S.R. 2009 Aug 10. Single-molecule sequencing of an individual human genome. Nat Biotechnol. [Epub ahead of print]
[Editor's Note: The SlingShot™ Kit from Fluidigm was used in this project to quantitate samples for sequencing]
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- van Erp, N.P., Eechoutem K., van der Veldt, A.A., et.al. 2009 Aug 10. Pharmacogenetic Pathway Analysis for Determination of Sunitinib-Induced Toxicity. J Clin Oncol. [Epub ahead of print]
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- Leong, D. E., Hahn-Windgassen, A., Foygel, K., Jun, S., Behr, B., Yao, M.W.M. 2009. Morpholino-mediated gene knockdown in the early mouse embryo. Nat Prot [Protocols Network]
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- Orina, J.N., Calcagno, A.M., Wu, C.P., et.al. 2009 July 7. Evaluation of current methods used to analyze the expression profiles of ATP-binding cassette transporters yields an improved drug-discovery database. Mol Cancer Ther. 8(7):2057-66
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- Sato, T., Onai, N., Yoshihara, H., Arai, F., Suda, T., Ohteki, T. 2009 Jun. Interferon regulatory factor-2 protects quiescent hematopoietic stem cells from type I interferon-dependent exhaustion. Nat Med. 15(6):696-700.
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- Haston, K.M., Tung, J.Y., Reijo Pera, R.A. 2009 May 21. Dazl functions in maintenance of pluripotency and genetic and epigenetic programs of differentiation in mouse primordial germ cells in vivo and in vitro. PLoS ONE. 4(5):e5654
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- Fan, H.C., Blumenfeld, Y.J., El-Sayed, Y.Y., Chueh, J., Quake, S.R. 2009 May. Microfluidic digital PCR enables rapid prenatal diagnosis of fetal aneuploidy. Am J Obstet Gynecol. 200(5):543.e1-7
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- Berndt, J.D., Biechele, T.L., Moon, R.T., Major, M.B. 2009 May 12. Integrative analysis of genome-wide RNA interference screens. Sci Signal. 2(70):pt4.
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- Weinstein, J.A., Jiang, N., White, R.A. 3rd, Fisher, D.S., Quake, S.R. 2009 May 8. High-throughput sequencing of the zebrafish antibody repertoire. Science. 324(5928):807-10.
[Editor's Note: The SlingShot™ Kit from Fluidigm was used in this project to quantitate samples for sequencing]
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- Bhat, S., Herrmann, J., Armishaw, P., Corbisier, P., Emslie, K.R. 2009 May. Single molecule detection in nanofluidic digital array enables accurate measurement of DNA copy number. Anal Bioanal Chem. 394(2):457-67.
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- Diehn, M., Cho, R.W., Lobo, N.A., et al. 2009 Apr 9. Association of reactive oxygen species levels and radioresistance in cancer stem cells. Nature. 458(7239):780-3.
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- Lee, J.E., Fusco, M.L., Saphire, E.O. 2009 Apr 2. An efficient platform for screening expression and crystallization of glycoproteins produced in human cells. Nat Protoc. 4(4):592-604.
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- Farber, C.R., Aten, J.A., Farber, E.A., et al. 2009 Mar 31. Genetic dissection of a major mouse obesity QTL (Carfhg2): Integration of gene expression and causality modeling. Physiol Genomics.
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- Garretta,T.P., Burgess, A.W., Gan, H.K., et al. 2009 Mar 31. Antibodies specifically targeting a locally misfolded region of tumor associated EGFR. PNAS. 106(13):5082-7
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- White, R.A. 3rd, Blainey, P.C., Fan, H.C., Quake, S.R. 2009 Mar 19. Digital PCR provides sensitive and absolute calibration for high throughput sequencing. BMC Genomics. 10(1):116.
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- Yung, T.K., Chan, K.C., Mok, T.S., Tong, J., To, K.F., Lo, Y.M. 2009 Mar 15. Single-Molecule Detection of Epidermal Growth Factor Receptor Mutations in Plasma by Microfluidics Digital PCR in Non-Small Cell Lung Cancer Patients. Clin Cancer Res. 15(6):2076-2084.
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- Lo, Y.M.D. 2009 Jan. Noninvasive prenatal detection of fetal chromosomal aneuploidies by maternal plasma nucleic acid analysis: a review of the current
state of the art. BJOG. 116:152–157.
[Editor’s Note: “..automated platforms for conducting digital PCR…” referenced in this paper (p156) is the Fluidigm BioMark Real Time System and Fluidigm 12.765 Digital Arrays”]
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2008
- Foygel, K., Choi, B., Jun, S., et al., 2008 Dec 31. A Novel and Critical Role for Oct4 as a Regulator of the Maternal-Embryonic Transition. PLoS ONE.3(12): e4109.
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- Zimmermann, B.G., Grill, S., Holzgreve, W., Zhong, X.Y., Jackson, L.G., Hahn, S., 2008 Dec. Digital PCR: a powerful new tool for noninvasive prenatal diagnosis? Prenat Diagn. 28(12):1087-93.
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- Golden, T.R., Hubbard, A., Dando, C., Herren, M.A., Melov, S., 2008 Dec. Age-related behaviors have distinct transcriptional profiles in Caenorhabditis elegans. Aging Cell. 7(6):850-65.
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- Major, M.B., Roberts, B.S., Berndt, J.D., et al., 2008 Nov 11. New regulators of Wnt/beta-catenin signaling revealed by integrative molecular screening. Sci Signal. 1(45):ra12.
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- Yao, Y., Higgs, B.W., Morehouse, C., et al., 2008 Nov 5. Development of potential pharmacodynamic and diagnostic markers for anti-IFN-α monoclonal antibody trials in systemic lupus erythematosus. Human Genomics and Proteomics, 2009: 16 pages
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- Kuchenbauer, F., Morin, R.D., Argiropoulos, B., et al., 2008 Nov, In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res. 18(11):1787-97.
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- Chang, C.P., Nagel, D., Zaghloul, M., Nov-Dec 2008, Go with the (micro) flow. IEEE Potentials. 27(6):17-25.
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- Dube, S., Mir, A., Jones, R.C., Ramakrishnan, R., Sun, G., 2008 Oct 27. Computation of Maximal Resolution of Copy Number Variation on a Nanofluidic Device using Digital PCR. arXiv:0809.1460v2 [q-bio.GN]
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- Fan, H.C., Blumenfeld, Y.J., Chitkara, U., Hudgins, L., and Quake, S.R. 2008 Oct 21. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. PNAS. 105(42):16266-71.
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- Jedrusik, A., Parfitt, D.E., Guo, G., et. al., 2008 Oct 1. Role of Cdx2 and cell polarity in cell allocation and specification of trophectoderm and inner cell mass in the mouse embryo. Genes Dev. 22(19):2692-706
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- Qin, J., Jones, R.C., Ramakrishnan, R. 2008 Oct. Studying copy number variations using a nanofluidic platform. Nucleic Acids Research. 36(18):e116.
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- Weisenberger, D.J., Trinh, B.N., Campan, M., et al. 2008 Aug. DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight. Nucleic Acids Research. 36(14):4689-98.
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- Lun, F.M., Chiu, R.W., Chan, K.C., Leung, T.Y., Lau, T.K., Lo, Y.M. 2008 Aug 14. Microfluidics Digital PCR Reveals a Higher than Expected Fraction of Fetal DNA in Maternal Plasma. Clinical Chemistry.
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- Dube, S., Qin, J., Ramakrishnan, R. 2008 Aug 6. Mathematical Analysis of Copy Number Variation in a DNA Sample Using Digital PCR on a Nanofluidic Device. PLoS ONE. 3(8): e2876.
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- Yao, Y., Richman, L., Morehouse, C., et al. 2008 Jul 16. Type I Interferon: Potential Therapeutic Target for
Psoriasis? PLoSONE. 3(7):e2737.
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- Oehler, V.G., Qin, J., Ramakrishnan, R., et. al. 2008 Jul 10. Absolute quantitative detection of ABL tyrosine kinase domain point mutations in chronic myeloid leukemia using a novel nanofluidic platform and mutation-specific PCR. Leukemia.
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- Lee, J.E., Fusco, M.L., Hessell, A.J., Oswald, W.B., Burton, D.R., Saphire, E.O. 2008 Jul 10. Structure of the Ebola virus glycoprotein bound to an antibody from a human survivor. Nature. 454(7201):177-82.
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- Iino, H., Naitow, H., Nakamura, Y., et. al. 2008 Jun 1. Crystallization screening test for the whole-cell project on Thermus thermophilus HB8. Acta Crystallogr Sect F Struct Biol Cryst Commun. 64(Pt 6):487-91.
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- Ishikawa, S., Umeda, T. 2008 May 31. Current status of CNV research and related methods. Clinical Genome Research (Japan). 229(9)
- Spurgeon, S.L., Jones, R. C., Ramakrishnan, R. 2008 Feb 27. High throughput gene expression measurement with real time PCR in a microfluidic dynamic array. PLoSONE. 3(2):e1662.
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- Heras, B., Kurz, M., Jarrott, R., et al. 2008 Feb 15. Staphylococcus aureus DsbA does not have a destabilizing disulfide. A new paradigm for bacterial oxidative folding. J Biol Chem. 15;283(7):4261-71
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- Kwon, H.J., Lagace, T.A., McNutt, M.C., Horton, J.D., Deisenhofer, J. 2008 Feb 12. Molecular basis for LDL receptor recognition by PCSK9. Proc Natl Acad Sci USA. 105(6):1820-5.
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2007
- Habicht, C., Templin, W.D., Willette, T.M., Fair, L.F., Raborn, S.W., and Seeb, L.W. 2007 Dec. Post-season stock composition analysis of Upper Cook Inlet sockeye salmon harvest, 2005-2007. Alaska Department of Fish and Game, Fishery Manuscript No.07-07, Anchorage.
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- Sindelka, R., Jonak, J., Hands, R., Bustin, S.A., and Kubista, M. 2007 Nov 26. Intracellular expression profiles measured by real-time PCR tomography in the Xenopus laevis oocyte. Nucleic Acids Research. 36(2): 387–392.
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- Heras, B., Kurz, M., Jarrott, R., et al. 2007 Nov 1. Expression and crystallization of DsbA from Staphylococcus aureus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 63(Pt 11):953-6.
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- Fan, H.C. , Quake, S.R. 2007 Oct 1. Detection of aneuploidy with digital polymerase chain reaction. Anal. Chem. 79(19):7576-9.
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- Chirifu, M., Hayashi, C., Nakamura, T. et al. 2007 Sep. Crystal structure of the IL-15-IL-15Ra complex, a cytokine-receptor unit presented in trans. Nature Immunology. 8(9):1001–7.
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- Spletter, M.L., Liu, J., Liu, J., 2007 Jul 16, Lola regulates Drosophila olfactory projection neuron identity and targeting specificity. Neural Develop. 2:14.
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- Yasui, N., Nogi, T., Kitao, T., Nakano, Y., Hattori, M., and Takagi, J. 2007 Jun 12. Structure of a receptor-binding fragment of reelin and mutational analysis reveal a recognition mechanism similar to endocytic receptors. Proc. Natl. Acad. Sci. USA. 104(24):9988-93.
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- Latham, C.F., Hu, S.H., Gee, C.L. et al. 2007 Jun 1. Crystallization and preliminary X-ray diffraction of the Munc18c-syntaxin4 1-29 complex. Acta Crystallograph Sect F Struct Biol Cryst Commun. 63(Pt 6):524-8.
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- Kothe, M., Kohls, D., Low, S., et al. 2007 May 22. Structure of the catalytic domain of human polo-like kinase 1. Biochemistry. 46(20):5960-71.
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- Hu, S.H., Latham, C.F., Gee, C.L., James, D.E., and Martin, J.L. 2007 May 22. Structure of the Munc18c/Syntaxin4 N-peptide complex defines universal features of the N-peptide binding mode of Sec1/Munc18 proteins. Proc. Natl. Acad. Sci. USA. 104(21):8773-8.
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2006
- Ottesen, E.A., Hong, J.W., Quake, S.R., and Leadbetter, J.R. 2006 Dec 1. Microfluidic digital PCR enables multigene analysis of individual environmental bacteria. Science. 314(5804):1464-7.
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- Warren, L., Bryder, D., Weissman, I.L., and Quake, S.R. 2006 Nov 21.Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR. Proc. Natl. Acad. Sci. USA. 103(47):17807-12.
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- English, C.M., Adkins, M.W., Carson, J.J., Churchill, M.E., and Tyler J.K. 2006 Nov 3. Structural basis for the histone chaperone activity of Asf1. Cell. 127(3):495-508.
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- Stevens, J., Blixt, O., Tumpey, T.M., Taubenberger, J.K., Paulson, J.C., and Wilson, I.A. 2006 Apr 21. Structure and receptor specificity of the hemagglutinin from an H5N1 influenza virus. Science. 312(5772):404-10.
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- Rowland, P., Blaney, F.E., Smyth, M.G., et al. 2006 Mar 17. Crystal structure of human cytochrome P450 2D6. J. Biol. Chem. 281(11):7614-22.
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2005
2004
- Hansen, C.L., Sommer, M.O., and Quake S.R. 2004 Oct 5. Systematic investigation of protein phase behavior with a microfluidic formulator. Proc. Natl. Acad. Sci. USA. 101(40):14431-6.
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- Xiao, T., Takagi, J., Coller, B.S., Wang, J.H., and Springer T.A. 2004 Nov 4. Structural basis for allostery in integrins and binding to fibrinogen-mimetic therapeutics. Nature. 432(7013):59-67.
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2003
- Liu, J., Hansen, C., and Quake, S.R. 2003 Sep 15. Solving the 'world-to-chip' interface problem with a microfluidic matrix. Analytical Chemistry. 75(18): 4718-4723.
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- Wheeler, A.R., Throndset, W.R., Whelan, R.J., et al. 2003 Jul 15. Microfluidic device for single-cell analysis. Analytical Chemistry. 75(14):3581-3586.
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2002
- Hansen, C.L., Skordalakes, E., Berger, J.M., and Quake S.R. 2002 Dec 24. A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion. Proc. Natl. Acad. Sci. USA. 99(26):16531-6.
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- Thorsen, T., Maerkl, S.J., and Quake, S.R. 2002 Oct 18. Microfluidic large-scale integration. Science. 298(5593):580-584.
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2001
2000
- Quake, S.R. and Scherer, A. 2000 Nov 24. From micro- to nanofabrication with soft materials. Science. 290(5496):1536-1540.
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- Unger, M.A., Chou, H.P., Thorsen, T., Scherer, A., and Quake, S.R. 2000 Apr 7. Monolithic microfabricated valves and pumps by multilayer soft lithography. Science. 288(5463):113-116.
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1999
- Fu, A.Y., Spence, C., Scherer, A., Arnold, F.H., and Quake, S.R. 1999 Nov. A microfabricated fluorescence-activated cell sorter. Nature Biotechnology 17(11):1109-1111.
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- Chou, H.P., Spence, C., Scherer, A., and Quake, S. 1999 Jan 5. A microfabricated device for sizing and sorting DNA molecules. Proc. Natl. Acad. Sci. USA. 96(1):11-13.
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