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Biotium Publications

Highlighted Citations

Single-Cell-Derived Tumor-Sphere Formation and Drug-Resistance Assay Using an Integrated Microfluidics

Pang, L., Ding, J., Ge, Y., Fan, J., & Fan, S. K. (2019). Single-Cell-Derived Tumor-Sphere Formation and Drug-Resistance Assay Using an Integrated Microfluidics. Analytical chemistry.
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Designing a bispecific, chimeric 4-1BB agonistic antibody for cancer immunotherapy

Compte M, Harwood SL, Muñoz IG, Navarro R, Zonca M, Perez-Chacon G, Erce-Llamazares A, Merino N, Tapia-Galisteo A, Cuesta AM, Mikkelsen K, Caleiras E, Nuñez-Prado N, Aznar MA, Lykkemark S, Martínez-Torrecuadrada J, Melero I, Blanco FJ, Bernardino de la Serna J, Zapata JM, Sanz L, Alvarez-Vallina L. A tumor-targeted trimeric 4-1BB-agonistic antibody induces potent anti-tumor immunity without systemic toxicity. Nat Commun. 2018 Nov 15;9(1):4809. doi:10.1038/s41467-018-07195-w.
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Super-resolution microscopy through thick biological samples

J. Kim, M. Wojcik, Y. Wang, K. Xu and X. Zhang, “Oblique plane single-molecule localization microscopy for thick samples,” bioRxiv (
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A timeline of critical events during reperfusion after ischemia in rat myocytes

Sciuto KJ, Deng SW, Moreno A, Zaitsev AV (2019) Chronology of critical events in neonatal rat ventricular myocytes occurring during reperfusion after simulated ischemia. PLoS ONE 14(2): e0212076.
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Linking lipid metabolism with APOE in Alzheimer’s disease pathology

Farmer BC, Kluemper J, Johnson LA. Apolipoprotein E4 Alters Astrocyte Fatty Acid Metabolism and Lipid Droplet Formation. Cells. 2019 Feb 20;8(2). pii: E182. doi: 10.3390/cells8020182.
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Cell migration and movement: key drivers of lung development/alveologenesis

Akram KM, Yates LL, Mongey R, Rothery S, Gaboriau DCA, Sanderson J, Hind M, Griffiths M, Dean CH. Live imaging of alveologenesis in precision-cut lung slices reveals dynamic epithelial cell behaviour. Nat Commun. 2019 Mar 12;10(1):1178.doi: 10.1038/s41467-019-09067-3.
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Total and viable bacteria and fungi in the International Space Station

Checinska Sielaff, A.,Urbaniak, C.,Mohan, G. B. M.,Stepanov, V. G.,Tran, Q.,Wood, J. M.,Minich, J.,McDonald, D.,Mayer, T.,Knight, R., et al. (2019). Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces. Microbiome 7, 50.
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Strength in numbers: enteric viruses in membrane clusters are more virulent

Santiana M, Ghosh S, Ho BA, Rajasekaran V, Du WL, Mutsafi Y, De Jésus-Diaz DA, Sosnovtsev SV, Levenson EA, Parra GI, Takvorian PM, Cali A, Bleck C, Vlasova AN, Saif LJ, Patton JT, Lopalco P, Corcelli A, Green KY, Altan-Bonnet N. Vesicle-Cloaked Virus Clusters Are Optimal Units for Inter-organismal Viral Transmission. Cell Host Microbe. 2018 Aug 8;24(2):208-220.e8. doi:10.1016/j.chom.2018.07.006.
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A new study claims to link oral pathogenic bacteria to Alzheimer’s disease pathology

Porphyromonas gingivalis in Alzheimer’s disease brains: Evidence for disease causation and treatment with small-molecule inhibitors. Dominy SS., Lynch C, et al. Science Advances 23 Jan 2019: Vol. 5, no. 1, eaau3333 DOI: 10.1126/sciadv.aau3333
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An in vitro approach to preclinical safety and efficacy evaluation of engineered TCR-based therapeutics

Harper J, Adams KJ, Bossi G, Wright DE, Stacey AR, Bedke N, et al. (2018) An approved in vitro approach to preclinical safety and efficacy evaluation of engineered T cell receptor anti-CD3 bispecific (ImmTAC) molecules. PLoS ONE 13(10):e0205491.
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Peculiarities of mitochondrial DNA of flagellate protozoans

Lukeš J, Wheeler R, Jirsová D, David V, Archibald JM. Massive mitochondrial DNA content in diplonemid and kinetoplastid protists. IUBMB Life. 2018 Oct 6. doi: 10.1002/iub.1894.
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Multicolor immunofluorescence detection of immune markers in FFPE tumor samples

Ijsselsteijn ME, Brouwer TP et al. Cancer immunophenotyping by 7 colour multispectral imaging without tyramide signal amplification. J Pathol Clin Res.2018 Sep 7. doi: 10.1002/cjp2.113.

Triple-fluorescence live cell imaging for anti-cancer drug screening

De P, Carlson JH et al. Triple Fluorescence staining to Evaluate Mechanism-based Apoptosis following Chemotherapeutic and Targeted Anti-cancer Drugs in Live Tumor Cells. Sci Rep. 2018;8(1):13192.doi: 10.1038/s41598-018-31575-3.

The spectrin-actin-based periodic cytoskeleton serves as a scaffold and molecular ‘‘ruler’’ during neural stem cell interactions

Hauser, Meghan, Rui Yan, Wan Li, Nicole A. Repina, David V. Schaffer, and Ke Xu. The Spectrin-Actin-Based Periodic Cytoskeleton as a Conserved Nanoscale Scaffold and Ruler of the Neural Stem Cell Lineage. Cell Reports 24, no. 6 (2018): 1512-1522.

Polysialic acid chains show affinity for ordered lipid raft regions of plasma membrane

Sapoń, K, Janas, T, Sikorski, AF, and Janas, T. (2018). Polysialic acid chains exhibit enhanced affinity for ordered regions of membranes. BBA-Biomembranes
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Antibiotic development – Tracking compound penetration into Gram-negative bacteria with click chemistry

Spangler B, Dovala D, Sawyer WS, Thompson KV, Six DA, Reck F, Feng BY. Molecular Probes for the Determination of Subcellular Compound Exposure Profiles in Gram-Negative Bacteria. ACS Infect Dis. 2018 Jun 15. doi:10.1021/acsinfecdis.8b00093.
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Quenching IF background allows detection of rare disseminated tumor cells (DTCs) in bone marrow

Haley D. Axelrod, H.D., Pienta, K.J., and Valkenburg, K.C. Optimization of Immunofluorescent Detection of Bone Marrow Disseminated Tumor Cells. Biological Procedures Online. 2018, 20:13.
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A new enzymatic oligo synthesis method

Palluk, et al. De novo DNA synthesis using polymerase-nucleotide conjugates. Nature Biotechnology volume36, pages645–650 (2018)
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PMAxx™ q-PCR: an effective tool for detection of seed-borne pathogens

Han S, Jiang N, Lv Q, Kan Y, Hao J, Li J, Luo L. Detection of Clavibacter michiganensis subsp. michiganensis in viable but nonculturable state from tomato seed using improved qPCR. PLoS One. 2018 May 3;13(5):e0196525. doi:10.1371/journal.pone.0196525.
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Fluoro-Gold™-Labeled Retinal Explant Culture for Neurotoxicity Screening Studies

FluoroGold-Labeled Organotypic Retinal Explant Culture for Neurotoxicity Screening Studies Smedowski A, Pietrucha-Dutczak M, Maniar T, Ajeleti M, Matuszek I, and Lewin-Kowalik J. Oxidative Medicine and Cellular Longevity. (2018), Article ID 2487473.
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Culprits in whole blood affecting quantitative PCR analysis: quenching of EvaGreen® fluorescence by haemoglobin

Read the full publication for more details: Sidstedt M, Hedman J, Romsos EL, Waitara L, Wadsö L, Steffen CR, Vallone PM, Rådström P. Inhibition mechanisms of hemoglobin, immunoglobulin G, and whole blood in digital and real-time PCR. Anal Bioanal Chem. 2018;410(10):2569-2583. doi: 10.1007/s00216-018-0931-z.
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Protein microarrays by 3D nanotexturing

Tsougeni K, Ellinas K, Koukouvinos G, Petrou PS, Tserepi A, Kakabakos SE, Gogolides E. Three-dimensional (3D) plasma micro-nanotextured slides for high performance biomolecule microarrays: Comparison with epoxy-silane coated glass slides. Colloids Surf B Biointerfaces. (2018), 165:270-277. doi:10.1016/j.colsurfb.2018.02.055.
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Flow-cytometry based screening for pro-longevity therapeutics

Sarnoski EA, Liu P, Acar M. A High-Throughput Screen for Yeast Replicative Lifespan Identifies Lifespan-Extending Compounds. Cell Rep. 2017 Nov 28;21(9):2639-2646. doi: 10.1016/j.celrep.2017.11.002.
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A method to count osteoblast cells using the DNA dye GelRed®

Yang, D.; Wijenayaka, A.R.; Atkins, G.J. A Fluorometric Method for the Quantification of Cell Number in Complex Differentiating Osteoblast-Osteocyte Cultures. Methods Protoc. 2018, 1, 14.
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Delving deeper into EvaGreen®-DNA interactions

Shoute LCT, Loppnow GR. Characterization of the binding interactions between EvaGreen dye and dsDNA. Phys Chem Chem Phys. 2018 Feb 14;20(7):4772-4780. doi:10.1039/c7cp06058k
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Nerve Terminal Dyes: Reliable and convenient optical probes for visualizing synaptic activity and dynamics

Lazarenko, R. M., DelBove, C. E. and Zhang, Q. (2018). Fluorescent Measurement of Synaptic Activity Using FM Dyes in Dissociated Hippocampal Cultured Neurons. Bio-protocol 8(2): e2690. DOI: 10.21769/BioProtoc.2690.
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Single-laser excitation, multicolor spectral imaging for single molecule tracking (SMT) in live cells

Huang T et al. Simultaneous Multicolor Single-Molecule Tracking with Single-Laser Excitation via Spectral Imaging. Biophys J. 2018;114(2):301-310. doi: 10.1016/j.bpj.2017.11.013.
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Combining droplet digital PCR (ddPCR) with the viability dye PMA to measure probiotic success

Droplet digital PCR improves absolute quantification of viable lactic acid bacteria in faecal samples. Gobert G, Cotillard A, Fourmestraux C, Pruvost L, Miguet J, Boyer M. J Microbiol Methods. (2018) 148:64-73. doi:10.1016/j.mimet.2018.03.004.
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UV-induced photoconversion artifacts of DAPI and Hoechst dyes causes green and red fluorescence emission

Karg, T.J. & Golic, K.G. Chromosoma (2017) Photoconversion of DAPI and Hoechst dyes to green and red-emitting forms after exposure to UV excitation.
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Smartphone-based POC diagnostics using fluorescent LAMP

(1) Chen W, Yu H, et al. Mobile Platform for Multiplexed Detection and Differentiation of Disease-Specific Nucleic Acid Sequences, Using Microfluidic Loop-Mediated Isothermal Amplification and Smartphone Detection. Anal Chem. 2017 Nov 7;89(21):11219-11226. doi: 10.1021/acs.analchem.7b02478. (2) Ganguli A, Ornob A, et al. Hands-free smartphone-based diagnostics for simultaneous detection of Zika, Chikungunya, and Dengue at point-of-care. Biomed Microdevices. 2017 Aug 22;19(4):73. doi: 10.1007/s10544-017-0209-9.
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A portable LED-based photoacoustic imaging system for near-infrared small animal imaging

Hariri A, Lemaster J, Wang J, Jeevarathinam AS, Chao DL, Jokerst JV. The characterization of an economic and portable LED-based photoacoustic imaging system to facilitate molecular imaging. Photoacoustics. 2017 Nov 26;9:10-20. doi:10.1016/j.pacs.2017.11.001.
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Effective quenching of red blood cell autofluorescence in tissue sections

Whittington, N. C., & Wray, S. (2017). Suppression of red blood cell autofluorescence for immunocytochemistry on fixed embryonic mouse tissue. Current Protocols in Neuroscience, 81,2.28.1–2.28.12. doi: 10.1002/cpns.35
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Interphase Chromosome Profiling – a novel, high-resolution and robust methodology for karyotyping by banded chromosome analysis

Babu R, Van Dyke DL, et al. Interphase Chromosome Profiling: A Method for Conventional Banded Chromosome Analysis Using Interphase Nuclei. Arch Pathol Lab Med. 2017 Oct 5. doi: 10.5858/arpa.2016-0621-OA.
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Refractive index optimization for live cell imaging

Boothe T, Hilbert L, Heide M, Berninger L, Huttner WB, Zaburdaev V, Vastenhouw NL, Myers EW, Drechsel DN, Rink JC. (2017). A tunable refractive index matching medium for live imaging cells, tissues and model organisms. Elife. 14;6. DOI: 10.7554/eLife.27240
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Multiple kinesins drive anterograde neuropeptide transport

Lim A, Rechtsteiner A, Saxton WM. (2017) Two kinesins drive anterograde neuropeptide transport. Mol Biol Cell. 28(24):3542-3553. https://doi: 10.1091/mbc.E16-12-0820
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Apoptosis probe to assess EGFR inhibitor sensitivity of non-small cell lung cancer

Guisier F, Bohn P, Patout M, Piton N, Farah I, Vera P, et al. (2017) In- and ex-vivo molecular imaging of apoptosis to assess sensitivity of non-small cell lung cancer to EGFR inhibitors using probe-based confocal laser endomicroscopy. PLoS ONE 12(7): e0180576.
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Whole animal staining with single-cell resolution

Kubota et al. (2017). Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution. Cell Reports 20, 236-250. DOI: 10.1016/j.celrep.2017.06.010
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Pocket-size closed-loop PCR system for POC diagnostics

B. Shu, C. Zhang, D. Xing. A sample-to-answer, real-time convective polymerase chain reaction system for point-of-care diagnostics. Biosensors and Bioelectronics, 2017. DOI:
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An infrared actin probe for single-molecule speckle (SiMS) microscopy

Yamashiro and Watanabe. An infrared actin probe for deep-cell electroporation-based single-molecule speckle (eSiMS) microscopy. Sensors. 17(7), 1545 (2017). Doi10.3390/s17071545
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Pathogen detection by massively parallel HRM analysis

Velez, D. O., et al. (2017). Massively parallel digital high resolution melt for rapid and absolutely quantitative sequence profiling. Scientific Reports, 7, Article number: 42326. doi:10.1038/srep42326
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Four-color nanoscale imaging of living and fixed cells with hyperSTED

Winter, F. R. et al. Multicolour nanoscopy of fixed and living cells with a single STED beam and hyperspectral detection. Sci. Rep. 7, 46492; doi: 10.1038/srep46492 (2017).
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Mutiplexed miRNA detection using Qbeads and GelRed®

Guo, Qingsheng and Bian, Feika and Liu, Yuqian and Qu, Xiaojun and Hu, Xianyun and Sun, Qingjiang. Hybridization chain reactions on silica coated Qbeads for the colorimetric detection of multiplex microRNAs.Chem. Commun. 2017. 53, 36, pp 4954-4957; doi: 10.1039/C7CC00462A
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Integrated imaging of cells in 3-dimensional culture reveals new nuclear structures

Danielle M. Jorgens, Jamie L. Inman, Michal Wojcik, Claire Robertson, Hildur Palsdottir, Wen-Ting Tsai, Haina Huang, Alexandre Bruni-Cardoso, Claudia S. López, Mina J. Bissell, Ke Xu, Manfred Auer. Deep nuclear invaginations are linked to cytoskeletal filaments - integrated bioimaging of epithelial cells in 3D culture. J Cell Sci 2017 130: 177-189; doi: 10.1242/jcs.190967
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Coaggregation of milk protein amyloid fibrils

Raynes, JK, et al. Coaggregation of κ-Casein and β-Lactoglobulin Produces Morphologically Distinct Amyloid Fibrils. Small. February 2017. DOI: 10.1002/smll.201603591
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Microbial genomics in a lunar/Mars simulated habitat

Mayer T, et al.Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation. Microbiome. June 2016. DOI: 10.1186/s40168-016-0167-0
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Chitosan microparticle preps simplify PCR from whole blood samples

Nanayakkara IA, Cao W, White IM. Simplifying Nucleic Acid Amplification from Whole Blood with Direct Polymerase Chain Reaction on Chitosan Microparticles. Analytical Chemistry. 2017. doi: 10.1021/acs.analchem.7b00274.
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Spatially extensive propagation of second messenger signaling through gap junctions in tissues

Escue, R. Kandasamy, K. and Parthasarathi, K. Thrombin Induces Inositol Trisphosphate-Mediated Spatially Extensive Responses in Lung Microvessels. Am J. Pathol 2017 doi: 10.1016/j.ajpath.2016.12.014
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Microfluidic biopsy trap for personalized cancer drug testing

Holton AB, Sinatra FL, Kreahling J, Conway AJ, Landis DA, Altiok S (2017) Microfluidic Biopsy Trapping Device for the Real-Time Monitoring of Tumor Microenvironment. PLoS ONE 12(1): e0169797. doi:10.1371/journal.pone.0169797
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Safer, more sensitive DNA dye for CsCl gradients

Gao J, Pan K, Li H, Fan X, Sun L, Zhang S, et al. (2017) Application of GelGreen™ in Cesium Chloride Density Gradients for DNA-Stable Isotope Probing Experiments. PLoS ONE 12(1): e0169554. doi:10.1371/journal.pone.0169554
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Tumor inflammation stabilizes PD-L1, promoting tumor survival

Lim, Seung-Oe et al. Deubiquitination and Stabilization of PD-L1 by CSN5. Cancer Cell 2016, Dec 12;30(6):925-939. DOI:
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Single-molecule DNA methylation detection with fluorescent AdoMet analogues

T. Gilboa, C. Torfstein, M. Juhasz, A. Grunwald, Y. Ebenstein, E. Weinhold, and A. Meller. Single-Molecule DNA Methylation Quantification Using Electro-optical Sensing in Solid-State Nanopores. ACS Nano 2016, 10, 8861−8870. DOI: 10.1021/acsnano.6b04748
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Can synthetic glycosaminoglycans prevent sinusitis?

Pulsipher A, Qin X, Thomas AJ, Prestwich GD, Oottamasathien S, Alt JA. Prevention of sinonasal inflammation by a synthetic glycosaminoglycan. Int Forum Allergy Rhinol. 2016. DOI: 10.1002/alr.21865
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Sensitive RT-LAMP detection of malaria infection using GelGreen® dye

Kemleu S, Guelig D, Eboumbou Moukoko C, Essangui E, Diesburg S, Mouliom A, et al. A Field-Tailored Reverse Transcription Loop-Mediated Isothermal Assay for High Sensitivity Detection of Plasmodium falciparum Infections. 2016, PLOS ONE 11(11), Nov 8;11(11):e0165506. doi: 10.1371/journal.pone.0165506.
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Evaluating the role of chitosan as an adjuvant for an intranasal HBV vaccine

Wang, Zhi-Biao, Pu Shan, Su-Zhen Li, Ya Zhou, Xia Deng, Ji-Lai Li, Yu Zhang, Jin-Shuang Gao, and Jing Xu. "The mechanism of action of acid-soluble chitosan as an adjuvant in the formulation of nasally administered vaccine against HBV." RSC Advances, 2016,6, 96785-96797.  doi: 10.1039/C6RA14419E.
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Evaluation of dental plaque and halitosis in dogs by PMA and qPCR

Jeusette IC, Román AM, Torre C, Crusafont J, Sánchez N, Sánchez MC, Pérez-Salcedo L, Herrera D. "24-hour evaluation of dental plaque bacteria and halitosis after consumption of a single placebo or dental treat by dogs." Am J Vet Res, June 2016, Vol. 77, No. 6 , Pages 613-619. doi: 10.2460/ajvr.77.6.613
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Single cell microarray for cell viability and comet assay in adherent cells

Lili Li, Weixing Wang, Mingyu Ding, Guoan Luo, and Qionglin Liang. Single-Cell-Arrayed Agarose Chip for in Situ Analysis of Cytotoxicity and Genotoxicity of DNA Cross-Linking Agents.Anal. Chem. DOI: 10.1021/acs.analchem.6b01008 (2016).
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Best dyes for quantification of low amounts of DNA

B. Bruijns, R. Tiggelaar, H. Gardeniers, Fluorescent cyanine dyes for the quantification of low amounts of dsDNA, Analytical Biochemistry (2016), doi: 10.1016/j.ab.2016.07.022
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RedDot™2 for Confocal Imaging of 3-D Tissue Architecture

van Royen ME, Verhoef EI, Kweldam CF, van Cappellen WA, Kremers GJ, Houtsmuller AB, van Leenders GJ. Three-dimensional microscopic analysis of clinical prostate specimens.Histopathology. 2016 Jun 29. doi: 10.1111/his.13022.
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Viability PCR for infectious norovirus in food and water samples

Randazzo, et al. Evaluation of viability PCR performance for assessing norovirus infectivity in fresh-cut vegetables and irrigation water. Int J Food Microbiol. 2016 Jul 16;229:106.
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CF™488 for 2-photon microscopy

Mercier L, et al. In vivo imaging of skeletal muscle in mice highlights muscle defects in a model of myotubular myopathy. IntraVital. 2016 Apr 6;5(1):e1168553. doi: 10.1080/21659087.2016.1168553.
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EvaGreen® PCR for Point-of-Care Ebola Diagnosis

Ahrberg CD, Manz A, Neužil P. Palm-Sized Device for Point-of-Care Ebola Detection. Anal. Chem., 2016, 88 (9), pp 4803–4807. doi: 10.1021/acs.analchem.6b00278
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