Research Publications Featuring Fluidigm Products

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Gene Expression

Valleron, W., Ysebaert, L., Berquet, L., Fataccioli, V., Quelen, C., Martin, A., Parrens, M., Lamant, L., de Leval, L., Gisselbrecht, C., Gaulard, P., Brousset, P. September 18, 2012. Small nucleolar RNA expression profiling identifies potential prognostic markers in peripheral T-Cell lymphoma. Blood
Rahimov, F., King, O.D., Leung, D.G., Bibat, G.M., Emerson, C.P., Kunkel, L.M., Wagner, K.R. September 17, 2012. Transcriptional profiling in facioscapulohumeral muscular dystrophy to identify candidate biomarkers. PNAS
Gruzdev, N., McClelland, M., Porwollik, S., Ofaim, S., Pinto, R., Saldinger-Sela, S. August 31, 2012. Global Transcriptional Analysis of Dehydrated Salmonella enterica Serovar Typhimurium. Applied and Environmental Microbiology
Gaedche, J., Grade, M., Camps, J. et al. July 31, 2012. The Rectal Cancer microRNAome - microRNA Expression in Rectal Cancer and Matched Normal Mucosa. Clinical Cancer Research
Hogan, V.E., Holweg, C.T.J., Choy, D.F., Kummerfeld, S.K., Hackney, J.A., Onno Teng, Y.K., Townsend, M.J., vanLaar, J.M. June 26, 2012. Pretreatment synovial transcriptional provile is associated with early and late clinical response in rheumatoid arthitis patients treated with rituximab. Ann Rheum Dis
Knudsen, A.R., kannerup, A-S., Dich, R., Funch-Jensen, P., Gronbaek, H., Kruhoffer, M., Mortensen, F.V. June 7, 2012. Ischemic pre- and postconditioning has pronounced effects on gene expression profiles in the rat liver after ischemia/reperfusion. American Journal of Physiology Gastronintestinal and Liver Physiology
Brevik, A., Lindeman, B., Rusnakova, V., Olsen, A-K., Brunborg, G., Duale, N. May 28, 2012. Paternal Benzo[a]pyrene Exposure Affects Gene Expression in the Early Developing Mouse Embryo. Toxicological Sciences
Valleron, W., Laprevotte, E., Gautier, E-F., Quelen, C., Delabesse, E., Agirre, X., Prosper, F., Kiss, T., Brousset, P. April 23, 2012. Specific small nucleolar RNA expression profiles in acute leukemia. Nature
Mariani, M., Franco Zannoni, G., Sioletic, S. et al. March 21, 2012. Gender Influences the Class III and V B-Tubulin Ability to Predict Poor Outcome in Colorectal Cancer. Clinical Cancer Research
Huelga, S.C., Yeo, G.W. et al. February 23, 2012. Integrative Genome-wide Analysis Reveals Cooperative Regulation of Alternative Splicing by hnRNP Proteins. Cell Reports
Reckzeh, K., Bereshchenko, O., Mead, A., Rehn, M., Kharazi, S., Jacobsen, S-E., Nerlov, C., Cammenga, J. February 9, 2012. Molecular and cellular effects of oncogene cooperation in a genetically accurate AML mouse model. Leukemia
Spitzer, T.L.B., Rojas, A., Zelenko, Z., Aghajanova, L., Erikson, D.W., Barragan, F., Meyer, M., Tamaresis, J.S., Hamilton, A.E., Irwin, J.C., Giudice, L.C. February 1, 2012. Perivascular Human Enometrial Mesenchymal Stem Cells Express Pathways Relevant to Self-Renewal, Lineage Specification, and Functional Phenotype. Biology of Reproduction
Walter, K., Holcomb, T. Januario, T., et al. January 19, 2012. DNA Methylation Profiling Defines Clinically Relevant Biological Subsets of Non-Small Cell Lung Cancer. Clinical Cancer Research
Miller, A.L., Sims, G.P., Brewah, Y.A., Rebelatto, M.C., Kearley, J., Benjamin, E., Keller, A.E., Brohawn, P., Herbst, R., Coyle, A.J., Humbles, A.A., Kolbeck, R. January 18, 2012. Opposing Roles of Membrane and Soluble Forms of the Receptor for Advanced Glycation End Products in Primary Respiratory Syncytial Virus Infection. The Journal of Infectious Disease
May-Panloup, P., Ferre´-L’Hoˆ tellier, V., Morinie`re, C., Marcaillou, C., Lemerle, S., Malinge, M.C., Coutolleau, A., Lucas, N., Reynier, P., Descamps, P., Guardiola, P. January 13, 2012. Molecular characterization of corona radiata cells from patients with diminished ovarian reserve using microarray and microfluidic-based gene expression profiling. Human Reproduction
Passtoors, W.M., Boer, J.M., Goeman, J.J., van den Akker, E.B., Deelen, J., Zwaan, B.J., Scarborough, A., van der Breggen, R., Vossen, R.H.A.M., Houwing-Duistermaat, J.J., van Ommen, G.J.B., Westendorp, R.G.J., van Heemst, D., de Craen, A.J.M., White, A.J., Gunn, D.A., Beekman, M., Slagboom, P.E. January 11, 2012. Transcriptional Profiling of Human Familial Longevity Indicates a Role for ASF1A and IL7R. PLoS ONE
Laurell H, Iacovoni JS, Abot A, Svec D, Maoret JJ, Arnal JF, Kubista M. January 6, 2012. Correction of RT-qPCR data for genomic DNA-derived signals with ValidPrime. Nucleic Acids Research
Rizkalla, S.W., Prifti, E., Cotillard, A., Pelloux, V., Rouault, C., Allouche, R., Laromiguière, M., Kong, L., Darakhshan, F., Massiera, F., Clement, K. January 2, 2012. Differential effects of macronutrient content in 2 energy-restricted diets on cardiovascular risk factors and adipose tissue cell size in moderately obese individuals: a randomized controlled trial. The American Journal of Clinical Nutrition
Rizkalla, S.W., Prifti, E., Cotillard, A., Pelloux, V., Rouault, C., Allouche, R., Laromiguière, M., Kong, L., Darakhshan, F., Massiera, F., Clement, K. January 2, 2012. Differential effects of macronutrient content in 2 energy-restricted diets on cardiovascular risk factors and adipose tissue cell size in moderately obese individuals: a randomized controlled trial. The American Journal of Clinical Nutrition
Suguitan, Jr., A.L., Matsuoka, Y., Lau, Y.F., Santos, C.P., Vogel, L., Cheng, L.I., Orandle, M., Subbaraoa, K. December 28, 2011. The Multibasic Cleavage Site of the Hemagglutinin of Highly Pathogenic A/Vietnam/1203/2004 (H5N1) Avian Influenza Virus Acts as a Virulence Factor in a Host-Specific Manner in Mammals. Journal of Virology
Agostini, J., Benoist, S., Seman, M., Julié, C., Imbeaud, S., Letourneur, F., Cagnard, N., Rougier, P., Brouquet, A., Zucman-Rossi, J., Laurent-Puig, P. December 24, 2011. Identification of molecular pathways involved in oxaliplatin-associated sinusoidal dilatation. Journal of Hepatology
Al-Garawi, A., Husain, M., Ilieva, D., Humbles, A.A., Kolbeck, R., Stampfli, M.R., O’Byrne, P.M., Coyle, A.J., Jordana, M. December 14, 2011. Shifting of Immune Responsiveness to House Dust Mite by Influenza A Infection: Genomic Insights. The Journal of Immunology
Homma, S., Chen, J.C.J., Rahimov, F., Beermann, M.L., Hanger, K., Bibat, G.M., Wagner, K.R., Kunkel, L.M., Emerson, C.P, Miller, J.B. November 23, 2011. A unique library of myogenic cells from facioscapulohumeral muscular dystrophy subjects and unaffected relatives: family, disease and cell function. European Journal of Human Genetics
Farb, M.G., Ganley-Leal, L., Mott, M., Liang, Y., Ercan, B., Widlansky, M.E., Bigornia, S.J., Fiscale, A.J., Apovian, C.M., Carmine, B., Hess, D.T., Vita, J.A., Gokce, N. November 17, 2011. Arteriolar Function in Visceral Adipose Tissue Is Impaired in Human Obesity. Arterioscler Thromb Vasc Biol.
Kooistra, M.K., Leduc, R.Y.M., Dawe, C.E., Fairbridge, N.A., Rasmussen, J., Man, J.H.Y., Bujold, M., Juriloff, D., King-Jones, K., McDermid, H.E. October 26, 2011. Strain-specific modifier genes of Cecr2-associated exencephaly in mice: genetic analysis and identification of differentially expressed candidate genes. Physiol Genomics
Guerau-de-Arellano, M., Alder, H., Ozer, H.G., Lovett-Racke, A., Racke, M.K. October 17, 2011. miRNA profiling for biomarker discovery in multiple sclerosis: From microarray to deep sequencing. Journal of Neuroimmunology
Deminice, R., da Silva, R.P., Lamarre, S.G., Brown, C., Furey, G,N., McCarter, S.A., Jordao, A.A., Kelly, K.B., King-Jones, K., Jacobs, R.L., Brosnan, M.E., and Brosnan, J.T. October 1, 2011. Creatine Supplementation Prevents the Accumulation of Fat in the Livers of Rats fed a High-Fat Diet. The Journal of Nutrition
Owczarczyk, K., Lal, P., Abbas, A.R., Wolslegel, K., Holweg, C., Dummer, W., Kelman, A., Brunetta, P., Lewin-Koh, N., Sorani, M., Leong, D., Fielder, P., Yocum, D., Ho, C., Ortmann, W., Townsend, M.J., and Behrens, T.W. September 22, 2011. A Plasmablast Biomarker for Nonresponse to Antibody Therapy to CD20 in Rheumatoid Arthritis. Science Translational Medicine
Virant-Klun, I., Skutella, T., Stimpfel, M., Sinkovec, J. December 6, 2011. Ovarian surface epithelium in patients with severe ovarian infertility: a potential source of cells expressing markers of pluripotent/multipotent stem cells. Journal of Biomedicine and Biotechnology
Pennesi,M.E., Stover, N.B., Stone,E.M., Chiang, P.W., and Weleber, R.G. September, 7, 2011. Residual Electroretinograms in Young Leber Congenital Amaurosis Patients with Mutations of AIPL1. Investigative Ophthalmology & Visual Science
Spitz, M.R., Gorlov, I.P., Amos, C.I., Dong, Q., Chen, W., Etzel, C.J., Gorlova, O.Y., Chang, D.W., Pu, X., Zhang, D., Wang, L., Cunningham, J.M., Yang, P., and Wu, X. August 25, 2011. Variants in Inflammation Genes Are Implicated in Risk of Lung Cancer in Never Smokers Exposed to Second-hand Smoke. Cancer Discovery
Botelho, F.M., Nikota, J.K., Bauer, C., Davis, N.H.E., Cohen, E.S., Anderson, I.K., Coyle, A.J., Kolbeck, R., Humbles, A.A., Stampfli, M.R., Sleeman, M.A. August 1, 2011. A mouse GM-CSF receptor antibody attenuates neutrophilia in mice exposed to cigarette smoke. European Respiratory Journal
Danilla, D.C., Anand, A., Sung, C.C., Heller, G., Leversha, M.A., Cao, L., Lilja, H., Molina, A., Sawyers, C.L., Fleisher, M., Scher, H.I. July 14, 2011. TMPRSS2-ERG Status in Circulating Tumor Cells as a Predictive Biomarker of Sensitivity in Castration-Resistant Prostate Cancer Patients Treated with Abiraterone Acetate. European Association of Urology
Yoo, A.S., Sun, A.X., Li, L., Shcheglovitov, A., Portmann, T., Li, Y., Lee-Messer, C.,
Dolmetsch, R.E., Tsien, R.W., Crabtree, G.R. July 13, 2011. MicroRNA-mediated conversion of human fibroblasts to neurons. Nature
Robic, A., Fève, K., Larzul,C., Billon, Y., van Son, M., Liaubet, L., Sarry, J., Milan, D., Grindflek, E. April 13, 2011. Expression levels of 25 genes in liver and testis located in a QTL region for androstenone on SSC7q1.2 Animal Genetics
Edery, P., Marcaillou, C., Sahbatou, M., Labalme, A., Chastang, J., Touraine, R., Tubacher, E., Senni, F., Bober, M.B., Nampoothiri, S., Jouk, P.S., Steichen, E., Berland, S., Toutain, A., Wise, C.A., Sanlaville, D., Rousseau, F., Clerget-Daroux, F., Leutenegger, A.L. April 8, 2011. Association of TALS Developmental Disorder with Defect in Minor Splicing Component. Science
Angeles Julaton, V.T., Reijo Pera, R.A. April 5, 2011. NANOS3 function in human germ cell development. Human Molecular Genetics
Lundberg, M., Thorsen, S. B., Assarsson, E., Villablanca, A., Tran, B., Gee, N. Knowles, M., Nielsen, B.S., Couto, E.G., Martin, R., Nilsson, O., Fermer, C., Schlingemann, J., Christensen, I.J., Nielsen, H., Ekström, B., Andersson, C., Gustafsson, M., Brunner, N., Stenvang, J., and Fredriksson, S. April 1, 2011. Multiplexed Homogeneous Proximity Ligation Assays for High-throughput Protein Biomarker Research in Serological Material. Molecular & Cellular Proteomics
Hogan, V., Holweg, C., Kummerfeld, S., Teng, Y.K.O., Townsend,M., and van Laar, J.M. 2011. Changes in gene expression in synovial tissue from refractory rheumatoid arthritis patients treated with rituximab. Annals of the Rheumatic Diseases
Nishikawa, M., Owaki, H., Fuji, T. April 14, 2011. Rheumatoid arthritis - treatment 180. Utility of Body Weight Classified Low-Dose Leflunomide in Japanese Rheumatoid Arthritis. Rheumatology
Jang, J.S., Simon, V., Feddersen, R., Rakhshan, F., Schultz, D., Zschunke, M., Lnigle, W., Kolbert, C., Jen, J. March 10, 2011. Quantitative miRNA Expression Analysis Using Fluidigm Microfluidic Dynamic Arrays. BMC Genomics
Bugarel, M., Beutin, L., Scheutz, F., Loukiadis, E., Fach, P. February 4, 2011. Identification of Genetic Markers for Differentiation of Shiga Toxin-Producing, Enteropathogenic, and Avirulent Strains of Escherichia coli 026. Applied and Evironmental Microbiology
Panula, S., Medrano, J.V., Kee, K., Bergström, R., Nguyen, H.N., Byers, B., Wilson, K.D., Wu, J.C., Simon, C., Hovatta, O., and Reijo Pera, R.A. December 23, 2011. Human germ cell differentiation from fetal- and adult-derived induced pluripotent stem cells. Human Molecular Genetics
Moltzahn, F., Hunkapiller, N., Mir, A.A., Imbar, T., Blelloch, R. January 1, 2011. High Throughput MicroRNA Profiling: Optimized Multiplex qRT-PCR at Nanoliter Scale on the Fluidigm Dynamic Array^TM IFCs. Medline
Moltzahn, F., Olshen, A.B., Baehner, L., Peek, A.S., Fong, L., Stoppler, H.J., Simko, J., Hilton, J.F., Carroll, P.R., and Blelloch, R. November 22, 2010. Microfluidic based multiplex qRT-PCR identifies diagnostic and prognostic microRNA signatures in sera of prostate cancer patients. Cancer Research
Wong, C.C., Loewke, K.E., Bossert, N.L., Behr, B., De Jonge, C.J., Baer T.M., & Reijo Pera, R.A. October 3, 2010. Non-invasive imaging of human embryos before embryonic genome activation predicts development to the blastocyst stage. Nature Biotechnology
Tehranchi, R., Woll, P.S., Anderson, K., et al. September 9, 2010. Persistent Malignant Stem Cells in del(5q) Myelodysplasia in Remission. The New England Journal of Medicine
Petriv, O.I., Kuchenbauer, F., Delaney, A.D., et al. August 11, 2010. Comprehensive microRNA expression profiling of the hematopoietic hierarchy. PNAS
Schoeffler, A.J., May, A.P. and Berger, J.M. July 31, 2010. A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function. Nucleaic Acids Research
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Hosokawa, K., Arai, F., Yoshihara, H., Iwasaki, H., Nakamura, Y., Gomei, Y. and Suda, T. July 29, 2010. Knockdown of N-cadherin suppresses the long-term engraftment of hematopoietic stem cells. BLOOD
Iwasaki, H., Arai, F., Kubota, Y., Dahl, M. and Suda, T. July 29, 2010. Endothelial protein C receptor-expressing hematopoietic stem cells reside in the perisinusoidal niche in fetal liver. BLOOD
Hennessy, B.T.J., Timms, K.M., Carey, M.S., et al. July 6, 2010. Somatic Mutations in BRCA1 and BRCA2 Could Expand the Number of Patients That Benefit From Poly (ADP Ribose) Polymerase Inhibitors in Ovarian Cancer. Journal of Clinical Oncology
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Petriv, O.I., Kuchenbauer, F., Delaney, A.D., Lecault, V., White, A., Kent, D., Marmolejo, L., Heuser, M., Berg, T., Copley, J., Sekulovec, S., Benz, C., Kuroda, E., Ho, V., Antignano, F., Halim, T., Giambra, V., Krystal, G., Takei, C.J.F., Weng, A.P., Piret, J., Eaves, C., Marra, M.A., Humphries, R.K. and Hansen, C.L. June 30, 2010. Comprehensive microRNA expression profiling of the hematopoietic hierarchy. Proceedings of the National Academy of Sciences of the United States of America
Tay, S., Hughey, J.J., Lee, T.K., Lipniacki, T., Quake, S.R. and Covert, M.W. June 27, 2010. Single-cell NF-kB dynamics reveal digital activation and analogue information processing. Nature
Kee, K., Flores, M., Cedars, M.I. and Pera, R. A .R. June 18, 2010. Human Primordial Germ Cell Formation Is Diminished by Exposure to Environmental Toxicants Acting through the AHR Signaling Pathway.Toxicological Sciences
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Hart, C.P. June 15, 2010. Product Focus: High-Content Screening and Imaging: Instrumentation, Analysis, and Applications. Journal of Biomolecular Sceening
McElroy, S.L., Byrne, J.A., Chavez, S.L., Behr, B., Hsueh, A.J.,Westphal, L.M., Reijo Pera, R.A. June 7, 2010. Parthenogenic Blastocysts Derived from Cumulus-Free In Vitro Matured Human Oocytes. PLoS ONE
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Cole, B.B., Smith, R.W., Jenkins, K.M., Graham, B.B., Reynolds, P.R. and Reynolds, S.D. June 3, 2010. Tracheal Basal Cells: A Facultative Progenitor Cell Pool. American Journal of Pathology
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Freedman, J.E., Larson, M.G., Tanriverdi, K., O'Donnell, C.J., Morin, K., Hakanson, A.S., Vasan, R.S., Johnson, A.D., Iafrati, M.D., and Benjamin E.J. May 14, 2010. Relation of Platelet and Leukocyte Inflammatory Transcripts to Body Mass Index in the Framingham Heart Study. A.H.A. Circulation
Van Baarsen, L.G., Wijbrandts, C.A., Rustenburg, F., Cantaert, T., van der Pouw Kraan, T.C., Baeten, D.L., Dijkmans, B.A., Tak, P.P., and Verweij, C.L. January 22, 2010. Regulation of IFN response gene activity during infliximab treatment in rheumatoid arthritis is associated with clinical response to treatment. Arthritis Research & Therapy
Wang, J., Ramakrishnan, R., Tang, Z., Fan, W., Kluge, A., Dowlati , A., Jones, R.C., Ma, P.C. Jan 19, 2010. Quantifying EGFR Alterations in the Lung Cancer Genome with Nanofluidic Digital PCR Arrays. Clinical Chemistry
Bujold, M., Gopalakrishnan, A., Nally, E., King-Jones, K. 2009 Nov 23. The nuclear receptor DHR96 acts as a sentinel for low cholesterol concentrations in Drosophila. Mol Cell Biol.
Jones, D., Yao, H., Romans, A., Dando, C., Pierce, S., Borthakur,G., Hamilton, A., Bueso-Ramos, C., Ravandi, F., Garcia-Manero, G., Kantarjian, H. 2009 Nov 11. Modeling interactions between leukemia-specific chromosomal changes, somatic mutations, and gene expression patterns during progression of core-binding factor leukemias. Wiley InterScience.
Lee, D.W., Rajagopalan, S., Siddiq, A., Gwiazda, R., Yang, L., Beal, M.F., Ratan, R.R. and Andersen, J.K. 2009 Oct 16. Inhibition of Prolyl Hydroxylase Protects against 1-Methyl-4-phenyl-,3,6-tetrahydropyridine-induced Neurotoxicity. The Journal of Biological Chemistry.
Helzer, K.T., Barnes, H.E., Day, L., Harvey, J., Billings, P.R., and Forsyth A. 2009 Sep 29. Circulating Tumor Cells Are Transcriptionally Similar to the Primary Tumor in a Murine Prostate Model. Cancer Research. [Epub ahead of print]
Byrne, J.A., Nguyen, H.N., Reijo Pera, R.A. 2009 Sept 23. Enhanced Generation of Induced Pluripotent Stem Cells from a Subpopulation of Human Fibroblasts. PLoS ONE.
J. P. C. da Cunhaa, P. A. F. Galantea, J. E. de Souzaa, R. F. et al . 2009 Sept 15. Bioinformatics construction of the human cell surfaceome. PNAS.
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
Sato, T., Onai, N., Yoshihara, H., Arai, F., Suda, T., Ohteki, T. 2009 June. Interferon regulatory factor-2 protects quiescent hematopoietic stem cells from type I interferon-dependent exhaustion. Nat Med. 15(6):696-700.
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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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.
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.
Yao, Y., Higgs, B.W., Morehouse, C., et al., 2008 Nov 5. Development of potential pharmacodynamic and diagnostic markers for anti-IFN-a monoclonal antibody trials in systemic lupus erythematosus. Human Genomics and Proteomics, 2009: 16 pages
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.
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.
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.
Chang, C.P., Nagel, D., Zaghloul, M., Nov-Dec 2008, Go with the (micro) flow. IEEE Potentials. 27(6):17-25.
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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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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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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Single-Cell Gene Expression

Tan, M.H., Au, K.F., Leong, D.E., Foygel, K., Wong, W.H., Yao, M.W. January 8, 2013. An Oct4-Sall4-Nanog network controls developmental progression in the pre-implantation mouse embryo. Molecular Systems Biology
McDavid, A., Finak, G., Chattopadyay, P.K., Dominguez, M., Lamoreaux, L., Ma, S.S., Roederer, M., Gottardo, R. December 24, 2012. Data Exploration, Quality Control and Testing in Single-Cell qPCR-Based Gene Expression Experiments. Bioinformatics
Flynn, J.M., Spusta, S.C., Rosen, C.J., Melov, S. December 10, 2012. Single cell gene expression profiling of cortical osteoblast lineage cells. Bone
Sen, A., Rothenberg, M.E., Mukherjee, G., Feng, N., Kalisky, T., Nair, N., Johnstone, I.M., Clarke, M.F., Greenberg, H.B. October 30, 2012. Innate immune response to homologous rotavirus infection in the small intestinal villous epithelium at single-cell resolution. PNAS
MacArthur, B.D., Ana Sevilla, A., Lenz, M., Müller,F-J., Schuldt, B.M., Schuppert, A.A., Ridden, S.J., Stumpf, P.S., Fidalgo, Ma'ayan, M.A., Wang, J. Lemischka, I.R. October 28, 2012. Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity. Nature
Livak, K.J., Wills, Q.F., Tipping, A.J., Datta, K., Mittal, R., Goldson, A., Sexton, D.W., Holmes, C.C. October 20, 2012. Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells. Methods
Lorthongpanich, C., Doris, T.P.Y., Limviphuvadh, V., Knowles, B.B., Solter, D. October 15, 2012. Developmental fate and lineage commitment of singled mouse blastomeres. Development and Stem Cells
Buganim, Y., Faddah, D.A., Cheng, A.W., Itskovich, E., Markoulaki, S., Ganz, K., Klemm, S.L., van Oudenaarden, A., Jaenisch, R. August 23, 2012. Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase. Cell
Shin, J.W., Suzuki, T., Ninomiya, N., Kishima, M., Hasegawa, Y., Kubosaki, A., Yabukami, H., Hayashizaki, Y., Suzuki, H. August 8, 2012. Establishment of single-cell screening system for the rapid identification of transcriptional modulators involved in direct cell reprogramming. Nucleic Acids Research
Narayanan G, Poonepalli A, Chen J, Sankaran S, Hariharan S, Yu YH, Robson P, Yang H, Ahmed S. July 26, 2012. Single-cell mRNA profling identifies progenitor subclasses in neurospheres. Stem Cells and Development
Surmacz, B., Fox, H., Gutteridge, A., Lubitz, S. Whiting, P. June 5, 2012. Directing Differentiation of Human Embryonic Stem Cells towards Anterior Neural Ectoderm Using Small Molecules. Stem Cells
Jeffrey, S.S., Powell, A.A. et al. May 7, 2012. Single Cell Profiling of Circulating Tumor Cells: Transcriptional Heterogeneity and Diversity from Breast Cancer Cell Lines. PLoS one
Sanchez-Freire, Ebert, A.D., Kalisky, T., Quake, S.R., Wu, J.C. April 5, 2012. Microfluidic single-cell real-time PCR for comparative analysis of gene expression traits. Nature Protocols
Luc, S., Jacobsen, S.E.W., et al. February 19, 2012. The earliest thymic T cell progenitors sustain B cell and myloid lineage potential. Nature Immunology
Pina, C., Fugazza, C., Tipping, A.J., Brown, J., Soneji, S., Teles, J., Peterson, C., Enver, T. February 19, 2012. Inferring rules of lineage commitment in haematopoiesis. Nature Cell Biology
Spike, B.T., Engle, D.D., Lin, J.C., Cheung, S.K., La, J., Wahl, G.M. February 2, 2012. A Mammary Stem Cell Population Identified and Characterized in Late Embryogenesis Reveals Similarities to Human Breast Cancer. Cell Stem Cell
Flynn, J. M., Santana, L. F., Melov, S. 2011. Single Cell Transcriptional Profiling of Adult Mouse Cardiomyocytes. J. Vis. Exp.
Oyolu, C., Zakharia, F., Baker, J. December 20, 2011. Distinguishing Human Cell Types Based on Housekeeping Gene Signatures. Stem Cells
Vincent, J.J., Ziwei Li, Z., Lee, S.A., Liu, X., Etter, M.O., Diaz-Perez, S.V., Taylor, S.K., Sofia Gkountela, S., Lindgren, A.G., Clark, A.T. December 15, 2011. Single Cell Analysis Facilitates Staging of Blimp1-Dependent Primordial Germ Cells Derived from Mouse Embryonic Stem Cells. PLoS ONE
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Citri, A., Pang, Z.P., Südhof, T.C., Wernig, M., Malenka, R.C. December 22, 2011. Comprehensive qPCR profiling of gene expression in single neuronal cells. Nature Protocols
Virant-Klun, I., Skutella, T., Stimpfel, M., Sinkovec, J. December 6, 2011. Ovarian surface epithelium in patients with severe ovarian infertility: a potential source of cells expressing markers of pluripotent/multipotent stem cells. Journal of Biomedicine and Biotechnology
Yin, H., Marshall, D. November 29, 2011. Microfluidics for single cell analysis. Current Opinion in Biotechnology
Dalerba, P., Kalisky, T., Sahoo, D., Rajendran, P.S., Rothenber, M.E., Leyrat, A., Sim, S., Okamoto, J., Johnston, D.M., Qian, D., Zabala, M., Bueno, J., Neff, N.F., Wang, J., Shelton, A.A., Visser, B., Hisamori, S.,Shimono, Y., van de Wetering, M., Clevers, H., Clarke, M.F., Quake, S.R. November 13, 2011. Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nature Biotechnology
Chu, L-F., Surani, A., Jaenisch, R., Zwaka, T.P. October 25, 2011. Blimp1 Expression Predicts Embryonic Stem Cell Development In Vitro. Current Biology
Vadigepalli R, Gonye GE, Paton JF, Schwaber JS. October 14, 2011. Adaptive transcriptional dynamics of A2 neurons and central cardiovascular control pathways. Experimental Physiology
Brevik, A., Rusnakova, V., Duale, N., Slagsvold, H.H., Olsen, A.K., Storeng, R., Kubista, M., Brunborg, G., Lindeman, B. September 29, 2011. Preconceptional paternal glycidamide exposure affects embryonic gene expression: Single embryo gene expression study following in vitro fertilization. Reproductive Toxicology
Marro, S., Pang, Z.P., Yang, N., Tsai, M.C., Qu, K., Chang, H.Y., Su¨ dhof, T.C., Wernig, M. September 29, 2011. Direct Lineage Conversion of Terminally Differentiated Hepatocytes to Functional Neurons. Cell Stem Cell
Levi, B., Longaker, M.T. et al. September 23, 2011. CD105 Protein Depletion Enhances Human Adipose-derived Stromal Cell Osteogenesis through Reduction of Transforming Growth Factor B1 (TGF-B1) Signaling. The Journal of Biological Chemistry
Kikushige, Y., Ishikawa, F., Miyamoto, T., Shima, T., Urata, S., Yoshimoto,G., Mori, Y., Iino, T., Yamauchi, T., Eto, T., Niiro, H., Iwasaki, H., Takenaka, K., Akashi, K. August 16, 2011. Self-Renewing Hematopoietic Stem Cell is the Primary Target in Pathogenesis of Human Chronic Lymphocytic Leukemia. Cancer Cell
Kharazi, S., Mead, A.J., Mansour, A., Hultquist, A., Boiers, C., Luc, S., Buza-Vidas, N., Ma, Z., Ferry, H., Atkinson, D., Rechzeh, K., Masson, K., Cammenga, J., Ronnstrand, L., Arai, F., Suda, T., Nerlov, C., Sitnicka, E., Jacobsen, S.E.W. August 2, 2011. Impact of gene dosage, loss of wild-type allele, and FLT3 ligand on FLt3-ITD-induced myeloproliferation. Blood
Yoo, A.S., Sun, A.X., Li, L., Shcheglovitov, A., Portmann, T., Li, Y., Lee-Messer, C.,
Dolmetsch, R.E., Tsien, R.W., Crabtree, G.R. July 13, 2011. MicroRNA-mediated conversion of human fibroblasts to neurons. Nature
Whitea, A.K., VanInsberghea, M., Petriva, O.I., Hamidia, M., Sikorskia, D., Marrae, M.A., Piretc, J., Apariciof, S., Hansena, C.L. June 17, 2011. High-throughput microfluidic single-cell RT-qPCR. Proceedings of the National Academy of Sciences
Buza-Vidas, N., Duarte, S., Luc, S., Bouriez-Jones, T., Woll, P.S., Waelgaard Jacobsen, S.E. June 13, 2011. GATA3 is redundant for maintenance and self-renewal of hematopoietic stem cells. Blood Journal of the American Society of Hematology
Buza-Vidas, N., Woll, P., Hultquist, A., Duarte, S., Lutteropp, M.I., Bouriez-Jones, T., Ferry, H., Luc, S., Waelgaard Jacobsen, S.E. May 31, 2011. FLT3 expression initiates in fully multipotent mouse hematopoietic progenitor cells. Blood Journal of the American Society of Hematology
Wang, Y.V., Leblanc, M., Fox, N., Mao, J-H., Tinkum, K.L., Krummel, K., Engle, D., Piwnica-Worms, D., Piwnica-Worms, H., Balmain, A., Kaushansky, K., and Wahl, G.M. May 26, 2011. Fine-tuning p53 activity through C-terminal modification significantly contributes to HSC homeostasis and mouse radiosensitivity. Genes & Development
Narsinh, K.H.....Wu, J.C. March 1, 2011. Single cell transcriptional profiling reveals heterogeneity of human induced pluripotent stem cells. Journal of Clinical Investigation
Aguilo, F., Avagyan, S., Labar, A.S., Sevilla, A., Lee, D-S., Kumar, P., Lemischka, I.R., Zhou, B.Y., Snoeck, H-W. Feburary 22, 2011. Prdm16 is a physiological regulator of hematopoietic stem cells. Blood
Flatz, L., Roychoudhuri, R., Honda, M., Filali-Mouhim, A., Goulet, J.P., Kettaf, N., Lin, M., Roederer, M., Haddad, E.K., Sekaly, R.P., Nabel, G.J. February 4, 2011. Single-cell gene-expression profiling reveals qualitatively distinct CD8 T cells elicited by different gene-based vaccines. Proceedings of the National Academy of Sciences (PNAS)
Fan, C.H., Wang, J., Potanina, A., Quake, S.R. December 10, 2010. Whole-genome molecular haplotyping of single cells. Nature Biotechnology
Narsinh, K.H., Sun, N., Sanchez-Freire, V., Lee, A.S., Almeida, P., Hu, S., Jan, T., Wilson, K.D., Leong, D., Rosenberg, J., Yao, M., Robbins, R.C., Wu, J.C. December 15, 2010. Single Cell Transcriptional Profiling Reveals Heterogeneity of Human Induced Pluripotent Stem Cells. Journal of Clinical Investigation
Nakamura, Y., Arai, F., Iwasaki, H., Hosokawa, K., Kobayashi, I., Gomei, Y., Matsumoto, Y., Yoshihara, H., Suda, T. September 2, 2010. Isolation and characterization of endosteal niche cell populations that regulate hematopoietic stem cells. Blood.
Guo, G., Huss, M., Tong, G.Q., Wang, C., Sun, L., Clarke, N.D., and Robson, P. April 20, 2010. Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst. Developmental Cell
Hosokawa, K., Arai, F., Yoshihara, H., Iwasaki, H., Hembree, M., Yin, T., Nakamura, Y., Gomei, Y., Takubo, K., Shiama, H., Matsuoka, S., Li, L.,Suda, T. March 5, 2010. Cadherin-based adhesion is a potential target for niche manipulation to protect hematopoietic stem cells in adult bone marrow. Cell Stem Cell
Ralston,A., Cox, B.J., Nishioka, N., Sasaki, H., Chea, E., Rugg-Gunn, P., Guo, G., Robson, P., Draper, J.S., and Rossant, J. February 1, 2010. Gata3 regulates trophoblast development downstream of Tead4 and in parallel to Cdx2. Development
Yuan, P., Han, J., Guo, G., Orlov, Y.L., Huss, M., Loh, Y., Yaw, L., Robson, P., Lim, B., and Ng, H. 2009 Nov 01. Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells. Genes Dev.
Nicholas, C.R., Haston, K.M., Grewall, A.K., Longacre, T.A. and Reijo Pera, R.A. 2009 Aug 20. Transplantation directs oocyte maturation from embryonic stem cells and provides a therapeutic strategy for female infertility. Human Molecular Genetics.
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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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Diehn, M., Cho, R.W., Lobo, N.A., et al. 2009 April 9. Association of reactive oxygen species levels and radioresistance in cancer stem cells. Nature. 9; 458: 780-783.
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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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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
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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SNP Genotyping

Lu, X, Gu, D., Qiang, B. et al. July 1, 2012. Genome-wide association study in Han Chinese identifies four new susceptibility loci for coronary artery disease. Nature Genetics
Bhat, S., Polanowski, A.M., Double, M.C., Jarman, S.N., Emslie, K.R. June 20, 2012. The Effect of Input DNA Copy Number on Genotype Call and Characterising SNP Markers in the Humpback Whale Genome Using a Nanofluidic Array. PLoS one
Byers, R.L., Harker, D.B., Yourstone, S.M., Maughan, P.J., Udall, J.A. January 18, 2012. Development and mapping of SNP assays in allotetraploid cotton. Theor. Appl. Genet.
Barnett, G.C, West, C.M.L. et al. December 13, 2011. Independent validation of genes and polymorphisms reported to be associated with radiation toxicity: a prospective analysis study. The Lancet Oncology
Verdier, V., Vera Cruz, C., Leach, J.E. September 22, 2011. Controlling rice bacterial blight in Africa: Needs and prospects. Journal of Biotechnology
K. Shitara, S. Ito, K. Misawa, Y. Ito, H. Ito, S. Hosono, M. Watanabe, K. Tajima, H. Tanaka, K. Muro, and K. Matsuo. June 20, 2011. Genetic polymorphism of IGF-I predicts recurrence in patients with gastric cancer who have undergone curative gastrectomy. Annals of Oncology
Chan, M., Chan, M.W., Loh, T.W., Law, H.Y., Yoon, C.S., Than, S.S., Chua, J.M., Wong, C.Y., Yong, W.S., Yap, Y.S., Ho, G.H., Ang, P, and Lee, A.S.G. May 2011. Evaluation of Nanofluidics Technology for High-Throughput SNP Genotyping in a Clinical Setting. Journal of Molecular Diagnostics
Namath, A., Patterson, A.J. March 1, 2011. Genetic Polymorphisms in Sepsis. Critical Care Nursing Clinics of North America
Maughan, P.J., Smith, S.M., Fairbanks, D.J., Jellen, E.N. March 1, 2011. Development, characterization and linkage mapping of single nucleotide polymorphisms in the gram Amaranths. The Plant Genome
Domingo, S., Cabeza, C.M., Pruvost, A., Torres, F., Salazar, J., del Mar Gutierrez, M., Mateo, M.G., Fontanet, A., Fernandez, I., Domingo, J.C., Villarroya, F., Vidal, F., and Baiget, M. January 31, 2011. Association of thymidylate synthase gene polymorphisms with stavudine triphosphate intracellular levels and lipodystrophy. American Society for Microbiology
Kocarnick, J.D., Hutter, C.M., Slattery, M.L., Berndt, S.I., Hsu, L., Duggan, D.J., Muehling, J., Caan, B.J., Beresford, S.A.A., Rajkovic, A., Sarto, G.E., Marshall, J.R., Hammad, N., Wallace, R.B., Makar, K.W., Prentice, R.L., Potter, J.D., Hayes, R.B., and Peters, U. October 26, 2010. Characterization of 9p24 Risk Locus and Colorectal Adenoma and Cancer: Gene-Environment Interaction and Meta-Analysis. Cancer Epidemiology, Biomarkers & Prevention
Baak-Pablo, R., Dezentje, V., Guchelaar, H., & van der Straaten, T. September 16, 2010. Genotyping of DNA Samples Isolated from Formalin-Fixed Paraffin-Embedded Tissues Using Preamplification. Journal of Molecular Diagnostics
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Pander, J., Wessels, J. A. M., Gelderblom, H., van der Straaten, T., Punt, C.J.A. & Guchelaar, H.-J. August 17, 2010 Pharmacogenetic interaction analysis for the efficacy of systemic treatment in metastatic colorectal cancer. Annals of Oncology
Paez, D., Pare, L., Espinosa, I., Salazar, J., Del Rio, E., Barnadas, A., Marcuello, E. and Baiget, M. May 18, 2010. Immunoglobulin G fragment C receptor polymorphisms and KRAS mutations: Are they useful biomarkers of clinical outcome in advanced colorectal cancer treated with anti-EGFR-based therapy? Cancer Science [Epub ahead of print]
Sagreiya, H., Berube, C,. Wen, A., Ramakrishnan, R., Mir, A., Hamilton, A., Altman, R.B. May 3, 2010. Extending and evaluating a warfarin dosing algorithm that includes CYP4F2 and pooled rare variants of CYP2C9. Pharmacogenetics and Genomics
Wang, J., Lin, M., Crenshaw, A., Hutchinson, A., Hicks, B., Yeager, M., Berndt, S., Huang, W.,Hayes, R.B., Chanock, S.J., Jones, R.C., and Ramakrishnan, R. 2009 Nov 28. High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays. BMC Genomics.
Seeb, J.E., Pascal, C.E., Ramakrishnan, R., Seeb, L.W. 2009. SNP genotyping by the 5'-nuclease reaction: advances in high-throughput genotyping with nonmodel organisms. Methods Mol Biol. [Epub ahead of print]
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]
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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Targeted Resequencing

Moonsamy, P.V., Williams, T., Bonella, P., Holcomb, C.L., Hoglunc, B.N., Hillman, G., Goodridge, D., Turenchalk, G.S., Blake, L.A., Daigle, D.A., Simen, B.B., Hamilton, A., May, A.P, Erlich, H.A. February 10, 2013. High throughput HLA genotyping using 454 sequencing and the Fluidigm Access Array system for simplified amplicon library preparation. Tissue Antigens
Halbritter, J., Diaz, K., Chaki, M., Porath, J.D., Tarrier, B., Fu, C., Innis, J.L., Allen, S.J., Lyons, R.H., Stefanidis, C.J., Omran, H., Soliman, N.A., Otto, E.A. October 1, 2012. High-throughput mutation analysis in patients with a nephronophthisis-associated ciliopathy applying multiplexed barcoded array-based PCR amplification and next-generation sequencing. Journal of Medical Genetics
Forshew, T., Murtaza, M., Parkinson, C., Gale, D., Tsui, D.W.Y., Kaper, F., Dawson, S.J., Piskorz, A.M.,
Jimenez-Linan, M., Bentley, D., Hadfield, J., May, A.P., Caldas, C., Brenton, J.D., Rosenfeld, N. May 31, 2012. Noninvasive Identification and Monitoring of Cancer Mutations by Targeted Deep Sequencing. Science Translational Medicine
Lohr, J.G., Golub, T.R., et al. February 17, 2012. Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proceedings of the National Academy of Sciences
Cronn, R., Knaus, B.J., Liston, A., Maughan, P.J., Parks, M., Syring, J.V., Udall, J. February 6, 2012. Targeted Enrichment Strategies for Next-Generation Plant Biology. American Journal of Botany

Hollants,S., Redeker, E.J.W., Matthijs, G. January 31, 2012. Microfluidic Amplification as a Tool for Massive Parallel Sequencing of Familial Hypercholesterolemia Genes. The American Association for Clinical Chemistry

Mertes, F., ElSharawy, A., Sauer, S., an Helvoort, J., van der Zaag, P.J., Franke, A., Nilsson, M., Lehrach H., Brookes, A.J. November 26, 2011. Targeted enrichment of genomic DNA regions for next-generation sequencing. Oxford Journals, Briefings in Functional Genomics

Zernant, J., Schubert, C., Im, K.M., Burke, T., Brown, C.M., Fishman, G.A., Tsang, S.H., Gouras, P., Dean, M., Allikmets, R. September 12, 2011. Analysis of the ABCA4 gene by next-generation sequencing. IOVS Investigative Ophthalmology & Visual Science
Schlipf, N.A., Schule, R., Klimpe, S., Karle, K.N., Synofzik, M., Schicks, J., Riessa, O., Schols, L., Bauer, P. June 13, 2011. Amplicon-based high-throughput pooled sequencing identifies mutations in CYP7B1 and SPG7 in sporadic spastic paraplegia patients. Clinical Genetics
Bybee, S.M., Bracken-Grissom, H., Haynes, B.D., Hermansen, R.A., Byers, R.L., Clement, M.J., Udall, J.A., Wilcox, E.R., Crandall, K.A. October 13, 2011. Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics. Genome Biology and Evolution
Etienne Paux, E., Sourdille, P., Mackay, I., Feuillet, C. October 1, 2011. Sequence-based marker development in wheat: Advances and applications to breeding. Biotechnology Advances
Grossmann, V., Kohlman, A., Eder, C., Haferlach, C., Kern, W., Cross, N.C., Haferlach, T., Schnittger, S. February 22, 2011. Molecular profiling of chronic myelomonocytic leukemia reveals diverse mutations in >80% of patients with TET2 and EZH2 being of high prognostic relevance. Leukemia
Zhang, J., Chiodini, R., Badr, A., Zhang, G. January 18, 2011. The impact of next-generation sequencing on genomics. Journal of Genetics and Genomics
Voelkerding, K.V., Dames, S., and Durtschi, J.D. September 5, 2010. Next Generation Sequencing for Clinical Diagnostics-Principles and Application to Targeted Resequencing for Hypertrophic Cardiomyopathy. Journal of Molecular Diagnostics
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Copy Number Variation/Digital Quantification/Digital PCR

Whale, A.S., Cowen, S., Foy, C.A., Huggett, J.F. March 5, 2013. Methods for Applying Accurate Digital PCR Analysis on Low Copy DNA Samples. PLoS ONE
Croville, G., Soubies, S.M., Barbieri, J., Klopp, C., Mariette, J., Bouchez, O., Camus-Bouclainville, C., Guerin, J-L. June 20, 2012. Field Monitoring of Avian Influenza Viruses: Whole-Genome Sequencing and Tracking of Neuraminidase Evolution Using 454 Pyrosequencing. Journal of Clinical Microbiology
Hoshino, T., Inagaki, F. July 27, 2012. Molecular quantification of environmental DNA using mcrofluidics and digital PCR. Systematic and Applied Microbiology
McGee, M.D., Day, N., Graham, J., Melov, S. April 30, 2012. cep-1/p53-dependent dysplastic pathology of the aging C. elegans gonad. Impact Journals: Aging

Hooli, B.V., Mohapatra, G., Mattheisen, M. et al. April 4, 2012. Role of common and rare APP DNA sequence variants in Alzheimer disease. Neurology

Barrett, A.N., McDonnell, T.C.R., Chan, K.C.A., Chitty, L.S. March 26, 2012. Digital PCR Analysis of Maternal Plasma for Noninvasive Detection of Sickle Cell Anemia. Clinical Chemistry

Pamp, S.J., Harrington, E.D., Quake, S.R. March 6, 2012. Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria. Genome Research

Whale, A.S., Huggett, J.F., Cowen, S., Speirs, V., Shaw, J., Ellison, S., Foy, C.A., Scott, D.J. February 14, 2012. Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation. Nucleic Acids Research

White, R.A. 3rd, Quake, S.R., Curr K. September 29, 2011. Digital PCR provides absolute quantitation of viral load for an occult RNA virus. Journal of Virological Methods

Jones, M.A., Bhide, S., Chin, E., Ng, B.G., Rhodenizer, D., Zhang, V.W., Sun, J.J., Tanner, A., Freeze, H.H., Hegde, M.R. August 1, 2011. Targeted polymerase chain reaction-based enrichment and next generation sequencing for diagnostic testing of congenital disorders of glycosylation. Genetics in Medicine

Tadmor, A.D., Ottesen, E.A., Leadbetter, J.R. and Phillips, R. July 1, 2011. Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR. Science

Tadmor, A.D., Ottesen, E.A., Leadbetter, J.R. and Phillips, R. May 4, 2011. Ultra-sensitive detection of drug resistant pandemic 2009 (H1N1) influenza A virus by Rare-Variant Sensitive High Resolution Melting. Science

Sanders, S.J., and State, M.W., et al. May 2, 2011. Multiple Recurrent De Novo CNVs, Including Duplications of the 7q11.23 Williams Syndrome Region, Are Strongly Associated with Autism. Neuron

Sanders, R., Huggett, J.F., Bushell, C.A., Cowen, S., Scott, D.J., Foy, C.A. March 30, 2011. Evaluation of Digital PCR for Absolute DNA Quantification. Analytical Chemistry

Goh, H.G., Lin, M., Fukushima, T., Saglio, G., Kim, D., Choi, S.Y., Kim, S.H., Lee, J., Lee, Y.S., Oh, S.M., Kim, D.W. February 22, 2011. Sensitive quantitation of minimal residual disease in chronic myeloid leukemia using nanofluidic digital polymerase chain reaction assay. Leukemia & Lymphoma

Blainey, P., and Quake, S. November 11, 2010. Digital MDA for enumeration of total nucleic acid contamination. Nucleic Acid Research
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Menzel, S., Qin, J., Vasavda, N., Thein, S.L., Ramakrishnan, R. September 24, 2010. Experimental Generation of SNP Haplotype Signatures in Patients with Sickle Cell Anaemia. PLoS One
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Snydera, T.M., Khush, K.K., Valantine, H.A., and Quake, S.R. September 15, 2010. Universal noninvasive detection of solid organ transplant rejection. PNAS

Blauw, H.M., Al-Chalabi, A., Andersen, P.M., et al. August 10, 2010. A large genome scan for rare CNVs in amyotrophic lateral sclerosis. Human Molecular Genetics

Hahn, S., Jackson, L.G., and Zimmermann, B.G. August 5, 2010. Prenatal diagnosis of fetal aneuploidies: post-genomic developments. Genome Medicine

Hahn, S. and Zimmermann, B.G. June 17, 2010. Cell-Free DNA in Maternal Plasma: Has the Size-Distribution Puzzle Been Solved? Clinical Chemistry
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Fan, C., Blumenfeld, Y.J., Chitkara, U., Hudgins, L., and Quake, S.R. June 17, 2010. Analysis of the Size Distributions of Fetal and Maternal Cell-Free DNA by Paired-End Sequencing. Clinical Chemistry

Spitali, P., Heemskerk, H., Vossen, R.H., Ferlini, A., den Dunnen, J.T., AC 't Hoen, P. and Aartsma-Rus, A. May 10, 2010. Accurate quantification of dystrophin mRNA and exon skipping levels in Duchenne Muscular Dystrophy. Laboratory Investigation

Burns, M.J., Burrell, A.M., and Foy, C.A. April 30, 2010. The applicability of digital PCR for the assessment of detection limits in GMO analysis. European Food Research Technology

Woyke, T., Tighe, D., Mavromatis, K., Clum, A., Copeland, A., Schackwitz, W., Lapidus, A., Wu, D., McCutcheon, J.P., McDonald, B.R., Moran, N.A., Bristow, J., Cheng, J. April 23, 2010. One Bacterial Cell, One Complete Genome. PLoS ONE

Weaver, S., Dube, S., Mir, A., Qin, J., Sun, G., Ramakrishnan, R., Jones, R.C., Livak K.J. April 1, 2010. Taking qPCR to a Higher Level: Analysis of CNV Reveals the Power of High Throughput qPCR to Enhance Quantitative Resolution. Methods.

Kato, M., Kawaguchi, T., Ishikawa, S., Umeda, T., Nakamichi, R., Shapero, M.H., Jones, K.W., Nakamura, Y., Aburatani, H., and Tsunoda, T. 2009 Dec 23. Population-genetic nature of copy number variations in the human genome. Human Molecular Genetics

Sikora, A., Zimmermann, B.G., Rusterholz, C., Birri, D., Kolla, V., Lapaire, O., Hoesli, I., Kiefer, V., Jackson, L., and Hahn, S. 2009. Detection of Increased Amounts of Cell-Free Fetal DNA with Short PCR Amplicons. Clinical Chemistry.

Corbisier, P., Bhat, S., Partis, L., Rui Dan Xie, V., Emslie, K.R., 2009 Oct 9. Absolute quantification of genetically modified MON810 maize (Zea mays L.) by digital polymerase chain reaction. Anal Bioanal Chem. [Epub ahead of print]

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]

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

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.

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.

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"]

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.

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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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. 54(10).
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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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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.

Ishikawa, S., Umeda, T. 2008 May 31. Current status of CNV research and related methods. Clinical Genome Research (Japan). 229(9).

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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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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Protein Crystallization

Davydova, N., Streltsov, V.A., Roufail, S., Lovrecz, G.O., Stacker, S.A., Adams, T.E., Achen, M.G. January 10, 2012. Preparation of human vascular endothelial growth factor-D for structural and preclinical therapeutic studies. Protein Expression and Purification
Olal, D., Kuehne, A., Bale, S., Halfmann, P., Hashiguchi, T., Fusco, M.L., Lee, J.E., King, L.B., Kawaoka, Y., Dye Jr., J.M., Saphire, E.O. December 14, 2012. Structure of an Antibody in Complex with Its Mucin Domain Linear Epitope That is Protective Against Ebola Virus. Journal of Virology
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.
Garrett,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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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.
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.
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
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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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.
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.
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.
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.
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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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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Lee C.C., Sui, G., Elizarov, A. et al. 2005 Dec 16. Multistep synthesis of a radiolabeled imaging probe using integrated microfluidics. Science. 310(5755):1793-1796.
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Segelke B. 2005 Apr. Macromolecular crystallization with microfluidic free-interface diffusion. Expert Rev. Proteomics. 2(2):165-72.
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.
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.
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.
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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Chou, H.P., Unger, M.A., and Quake, S.R. 2001 Dec. A microfabricated rotary pump. Biomedical Microdevices. 3(4): 323-330.
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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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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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