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Biotium Publications & Product Reference Lists

Reference Lists

Biotium Publications

Characterization of EvaGreen Dye and the implication of its physicochemical properties for qPCR applications

Mao, et al. BMC Biotechnology 7, 76 (2007)

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Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells

Nocker, et al. Journal of Microbiological Methods 67 (2006)

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DEVD-NucView488: a novel class of enzyme substrates for real-time detection of caspase-3 activity in live cells

Cen, et al. The FASEB Journal 22, 7 (2008)

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Tips for Avoiding Artifacts from UV Photoconversion of DAPI

Roberts, L. Microscopy Today, 27, 5 (2019)

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Small molecular fluorescence dyes for immuno cell analysis

Jiang, J., Li, X., Mao, F., Wu, X., & Chen, Y. Analytical Biochemistry, 114063 (2020)

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Highlighted Citations

ExoBrite™ CTB EV Stain assists in evaluating engineered EVs for targeted drug delivery against triple-negative breast cancer

Bhullar AS, Jin K, Shi H, Jones A, Hironaka D, Xiong G, Xu R, Guo P, Binzel DW, Shu D. Engineered extracellular vesicles for combinatorial TNBC therapy: SR-SIM-guided design achieves substantial drug dosage reduction. Mol Ther. 2024 Oct 5:S1525-0016(24)00658-0. doi: 10.1016/j.ymthe.2024.09.034. Epub ahead of print. PMID: 39369270.

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Tardigrade-derived protein shown to improve adipose stem cell survival against various stressors

Rolsma, J.L., Darch, W., Higgins, N.C. et al. The tardigrade-derived mitochondrial abundant heat soluble protein improves adipose-derived stem cell survival against representative stressors. Sci Rep 14, 11834 (2024). https://doi.org/10.1038/s41598-024-62693-w

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Arl2 GTPase associates with the centrosomal protein Cdk5rap2 to regulate cortical development via microtubule organization

Ma D, Lin K-Y, Suresh D, Lin J, Gujar MR, Aung HY, et al. (2024) Arl2 GTPase associates with the centrosomal protein Cdk5rap2 to regulate cortical development via microtubule organization. PLoS Biol 22(8): e3002751. https://doi.org/10.1371/journal.pbio.3002751

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The DNA-PAINT palette: a comprehensive performance analysis of fluorescent dyes

Steen, P.R., Unterauer, E.M., Masullo, L.A. et al. The DNA-PAINT palette: a comprehensive performance analysis of fluorescent dyes. Nat Methods 21, 1755–1762 (2024). https://doi.org/10.1038/s41592-024-02374-8

APOE4/4 is linked to damaging lipid droplets in Alzheimer’s disease microglia

Haney, M.S., Pálovics, R., Munson, C.N. et al. APOE4/4 is linked to damaging lipid droplets in Alzheimer’s disease microglia. Nature 628, 154–161 (2024). https://doi.org/10.1038/s41586-024-07185-7

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Computational Investigations into Two-Photon Fibril Imaging Using the DANIR-2c Probe

N. Arul Murugan, Robert Zaleśny. Computational Investigations into Two-Photon Fibril Imaging Using the DANIR-2c Probe. J. Phys. Chem. B, 127, 14, 3119–3125 (2023). https://doi.org/10.1021/acs.jpcb.2c07783

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Intraocular liver spheroids for non-invasive high-resolution in vivo monitoring of liver cell function

Lazzeri-Barcelo, F., Oliva-Vilarnau, N., Baniol, M. et al. Intraocular liver spheroids for non-invasive high-resolution in vivo monitoring of liver cell function. Nat Commun 15, 767 (2024). https://doi.org/10.1038/s41467-024-45122-4

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Anti-cancer target hRpn13 regulates proteome and transcriptome through epigenetic factors

Osei-Amponsa et al. (2023) Molecular Cell 84, 522–537 (2024) Published by Elsevier Inc., 2023, https://doi.org/10.1016/j.molcel.2023.11.035

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A novel type of large EVs containing lipid droplets and mitochondria is released during melanoma cell division

Karbanová, J., Deniz, I. A., Wilsch-Bräuninger, M., de Sousa Couto, R. A., Fargeas, C. A., Santos, M. F., ... & Corbeil, D. (2024). Extracellular lipidosomes containing lipid droplets and mitochondria are released during melanoma cell division. Cell Communication and Signaling, 22(1), 57.

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Distinct neuroinflammatory signatures exist across genetic and sporadic amyotrophic lateral sclerosis cohorts

Rifai, O.M., O’Shaughnessy, J., et al (2023) Distinct neuroinflammatory signatures exist across genetic and sporadic amyotrophic lateral sclerosis cohorts (2023). Brain, Volume 146, Issue 12, 2023, 5124–5138, DOI: 10.1093/brain/awad243

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Gene regulation in progenitor cells is mediated through NUP98 and RAE1 chromatin binding in a HDAC dependent manner

Neely, A.E., Blumensaadt, L.A., Ho, P.J. et al. (2023) NUP98 and RAE1 sustain progenitor function through HDAC-dependent chromatin targeting to escape from nucleolar localization. Commun Biol 6, 664. https://doi.org/10.1038/s42003-023-05043-2

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Post-Printing Modifications in 3D Bioprinting using Clickable Bioinks

Tournier, P., Saint‐Pé, G., Lagneau, N., Loll, F., Halgand, B., Tessier, A., ... & Delplace, V. (2023). Clickable Dynamic Bioinks Enable Post‐Printing Modifications of Construct Composition and Mechanical Properties Controlled over Time and Space. Advanced Science, 10(30), 2300055. https://doi.org/10.1002/advs.202300055

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Advancing digital PCR-HRM assays for better pathogen identification

Lee, P.W., Chen, L., Hseih, K. et al (2023) Harnessing Variabilities in Digital Melt Curves for Accurate Identification of Bacteria (2023). Analytical Chemistry 2023 95 (42), 15522-15530. DOI: 10.1021/acs.analchem.3c01654

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Biotium CF® Dyes aid in the discovery of MSC‑associated migrasomes as a novel source of chemoattractant for cells of hematopoietic origin

Deniz, I. A., Karbanová, J., Wobus, M., Bornhäuser, M., Wimberger, P., Kuhlmann, J. D., & Corbeil, D. (2023). Mesenchymal stromal cell-associated migrasomes: a new source of chemoattractant for cells of hematopoietic origin. Cell Communication and Signaling, 21(1), 1-17. https://doi.org/10.1186/s12964-022-01028-6

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Rapid Detection of Predominant SARS-CoV-2 Variants Using EvaGreen® Dye in Multiplex High-Resolution Melting Analysis

Sun, L., Wang, L., Zhang, C. et al (2023). Rapid detection of predominant SARS-COV-2 variants using multiplex high-resolution melting analysis. Microbiology Spectrum (2023). https://journals.asm.org/doi/10.1128/spectrum.00055-23

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The molecular architecture of the photoreceptor active zone resolved with CF®660C Dye in MINFLUX

Grabner, C. P., Jansen, I., Neef, J., Weihs, T., Schmidt, R., Riedel, D., ... & Moser, T. (2022). Resolving the molecular architecture of the photoreceptor active zone with 3D-MINFLUX. Science Advances, 8(28), eabl7560. DOI: 10.1126/sciadv.abl7560

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Mix-n-Stain™ labeling used in epitope mapping of novel NANOBODIES® for the Alzheimer’s-related receptor SORLA

Monti, G., Vincke, C., Lunding, M., Jensen, A. M. G., Madsen, P., Muyldermans, S., ... & Andersen, O. M. (2023). Epitope mapping of nanobodies binding the Alzheimer’s disease receptor SORLA. Journal of Biotechnology. https://doi.org/10.1016/j.jbiotec.2023.08.005

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Enhanced axial resolution in three-dimensional structured illumination microscopy using CellBrite® Fix Membrane Dyes

Li, X., Wu, Y., Su, Y., Rey-Suarez, I., Matthaeus, C., Updegrove, T. B., ... & Shroff, H. (2023). Three-dimensional structured illumination microscopy with enhanced axial resolution. Nature Biotechnology, 1-13. https://doi.org/10.1038/s41587-022-01651-1

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Development of novel PE and APC near-infrared tandem fluorochromes for use in spectral flow cytometry

Seong, Y., Nguyen, D. X., Wu, Y., Thakur, A., Harding, F., & Nguyen, T. A. (2022). Novel PE and APC tandems: Additional near‐infrared fluorochromes for use in spectral flow cytometry. Cytometry Part A, 101(10), 835-845. https://doi.org/10.1002/cyto.a.24537

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High-resolution characterization of centriole morphology, dynamics, and abnormalities using correlative STORM and electron microscopy

Bowler, M., Kong, D., Sun, S., Nanjundappa, R., Evans, L., Farmer, V., ... & Loncarek, J. (2019). High-resolution characterization of centriole distal appendage morphology and dynamics by correlative STORM and electron microscopy. Nature communications, 10(1), 993. Vásquez-Limeta, A., Lukasik, K., Kong, D., Sullenberger, C., Luvsanjav, D., Sahabandu, N., ... & Loncarek, J. (2022). CPAP insufficiency leads to incomplete centrioles that duplicate but fragment. Journal of Cell Biology, 221(5), e202108018.

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Exosome-delivered miRNA promotes breast cancer progression in African Americans by activating cancer-associated fat cells

Zhao, D., Wu, K., Sharma, S., Xing, F., Wu, S. Y., Tyagi, A., ... & Watabe, K. (2022). Exosomal miR-1304-3p promotes breast cancer progression in African Americans by activating cancer-associated adipocytes. Nature Communications, 13(1), 7734. https://www.nature.com/articles/s41467-022-35305-2

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Usage of the NanoString® platform to evaluate the effect of RNA integrity on gene expression profiling of FFPE samples

Manjunath, H. S., Al Khulaifi, M., Sidahmed, H., Ammar, A., Vadakekolathu, J., Rutella, S., et al. Gene Expression Profiling of FFPE Samples: A Titration Test. Technology in Cancer Research & Treatment, 21, 15330338221129710 (2022). https://doi.org/10.1177/15330338221129

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Biotium dyes and antibodies help to demonstrate a novel anchoring strategy for expansion microscopy

Klimas, A., Gallagher, B. R., Wijesekara, P., et al. Magnify is a universal molecular anchoring strategy for expansion microscopy. Nat Biotechnol 1-12 (2023). https://doi.org/10.1038/s41587-022-01546-1

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GelRed® analysis of contaminating endogenous cfDNA from FBS

Werner, B., Warton, K., & Ford, C. E. Endogenous cell-free DNA in fetal bovine serum introduces artifacts to in vitro cell-free DNA models. BioTechniques, 73(5), 219-226 (2022). https://doi.org/10.2144/btn-2022-0040

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Biotium dyes help demonstrate an acousto-optic tunable filter (AOTF)-based system for excitation spectral microscopy super-multiplexing

Chen, K., Li, W., & Xu, K. (2022). Super-multiplexing excitation spectral microscopy with multiple fluorescence bands. Biomedical Optics Express, 13(11), 6048-6060. https://doi.org/10.1364/BOE.473241

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Glucose oxidase-dependent deposition of fluorochromized tyramide (FT-GO) for sensitive multiplex immunofluorescence and in situ hybridization labeling

Yamauchi, K., Okamoto, S., Ishida, Y., et al. Fluorochromized tyramide-glucose oxidase as a multiplex fluorescent tyramide signal amplification system for histochemical analysis. Scientific Reports, 12(1), 1-12 (2022). https://doi.org/10.1038/s41598-022-19085-9

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Nuclei bypass intercellular obstacles by deforming around them with deep local invaginations mediated by lamin A/C

Katiyar, A., Zhang, J., Antani, J. D. et al. The nucleus bypasses obstacles by deforming like a drop with surface tension mediated by lamin A/C. Advanced Science, 9(23), 2201248 (2022). https://doi.org/10.1002/advs.202201248

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Fluoroamphiphile-based nanocarriers for intracellular drug delivery and organelle targeting

Liu, Y., Zhang, J., Tu, Y., & Zhu, L. Potential-independent intracellular drug delivery and mitochondrial targeting. ACS nano, 16(1), 1409-1420 (2021). https://doi.org/10.1021/acsnano.1c09456

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An optimized universal hairpin primer system for RT-qPCR-based quantification of miRNA expression

He, F., Ni, N., Wang, H., et al. OUHP: an optimized universal hairpin primer system for cost-effective and high-throughput RT-qPCR-based quantification of microRNA (miRNA) expression. Nucleic acids research, 50(4), e22-e22 (2022). https://academic.oup.com/nar/article/50/4/e22/6440322

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Single particle counting using fluorescent antibodies demonstrated as a promising diagnostic tool for neurodegenerative diseases

Blömeke, L., et al. Quantitative detection of α-Synuclein and Tau oligomers and other aggregates by digital single particle counting. npj Parkinson's Disease 8.1 1-13 (2022). https://doi.org/10.1038/s41531-022-00330-x

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TrueBlack® Lipofuscin Autofluorescence Quencher is the preferred quencher for detection of mRNA in human neuronal populations

May‐Zhang, A. A., Benthal, J. T., & Southard‐Smith, E. M. (2022). Hybridization Chain Reaction for mRNA Localization in Single Cells from Mouse and Human Cryosections. Current Protocols, 2(5), e439.https://doi.org/10.1002/cpz1.439

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A new high-throughput and broadband photoacoustic microscopy technique validated with near-infrared CellBrite® Dyes

Takeshi H., Kazuyoshi T., Manami M., Shinpei O., Toshihiro K., Miya I. (2022). Spectroscopic photoacoustic microscopic imaging during single spatial scan using broadband excitation light pulses with wavelength-dependent time delay. Photoacoustics, 26, 2213-5979. https://doi.org/10.1016/j.pacs.2022.100364

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A chip-based assay for detection and avidity assessment of SARS-CoV-2 antibodies in serum and saliva

Liu, T., Hsiung, J., Zhao, S., Kost. et al. Quantification of antibody avidities and accurate detection of SARS-CoV-2 antibodies in serum and saliva on plasmonic substrates. Nature Biomedical Engineering 4:12, 4(12), 1188–1196 (2020). https://doi.org/10.1038/s41551-020-00642-4

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Introduction of extracellular matrix inhibits glioma cell proliferation

Murdock, M. H., Hussey, G. S., Chang, J. T., Hill, R. C., Nascari, D. G., Rao, A. V., Hansen, K. C., Foley, L. M., Hitchens, T. K., Amankulor, N. M., & Badylak, S. F. (2022). A liquid fraction of extracellular matrix inhibits glioma cell viability in vitro and in vivo. Oncotarget, 13, 426–438. https://doi.org/10.18632/oncotarget.28203

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GelRed® used to assess efficiency of metallohelices as gene delivery vectors

Malina, J., Kostrhunova, H., Novohradsky, V. et al. (2022) Metallohelix vectors for efficient gene delivery via cationic DNA nanoparticles, Nucleic Acids Research. https://doi.org/10.1093/nar/gkab1277

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Multiview confocal microscopy protocol for improved imaging in thick samples

Wu, Y., Han, X., Su, Y. et al. (2021) Multiview confocal super-resolution microscopy. Nature. https://doi.org/10.1038/s41586-021-04110-0

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UC Berkeley and Biotium identify dye modifications for superior fluorescence photoswitching in STORM

Wang, B., Xiong, M., Susanto, J., Li, X., Leung, W.-Y., & Xu, K. (2021). Transforming Rhodamine Dyes for (d)STORM Super-Resolution Microscopy via 1,3-Disubstituted Imidazolium Substitution. Angewandte Chemie International Edition. https://doi.org/10.1002/ANIE.202113612

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Endocytosis of cationic molecules requires Rab14, but not Rab5 and Rab7

Trofimenko, E., Homma, Y., Fukuda, M., & Widmann, C. (2021). The endocytic pathway taken by cationic substances requires Rab14 but not Rab5 and Rab7. Cell Reports, 37(5), 109945. https://doi.org/10.1016/j.celrep.2021.109945

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TrueBlack® added to resin embedding medium improves signal-to-noise in brain tissue

Ren, M., Tian, J., Sun, Q., Chen, S., Luo, T., Jia, X., Jiang, T., Luo, Q., Gong, H., & Li, X., (2021). Plastic embedding for precise imaging of large-scale biological tissues labeled with multiple fluorescent dyes and proteins. Biomed. Opt. Express 12, 6730-6745. https://doi.org/10.1364/BOE.435120

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Novel nanoformulated antiretroviral therapy for HIV treatment with improved drug targeting

Martinez-Skinner AL, Araínga MA, Puligujja P, Palandri DL, Baldridge HM, Edagwa BJ, et al. (2015) Cellular Responses and Tissue Depots for Nanoformulated Antiretroviral Therapy. PLOS One 10(12): e0145966. https://doi.org/10.1371/journal.pone.0145966

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Viability PCR with PMA validated for determination of infectious SARS-CoV-2 viruses

Hong, W., Xiong, J., Nyaruaba, R., Li, J., Muturi, E., Liu, H., Yu, J., Yang, H., & Wei, H. (2021). Rapid determination of infectious SARS-CoV-2 in PCR-positive samples by SDS-PMA assisted RT-qPCR. The Science of the total environment, 797, 149085. Advance online publication. https://doi.org/10.1016/j.scitotenv.2021.149085

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Voltage dye Di-4-ANEPPS used to develop improved optical mapping of rat hearts

Ramlugun, G. S., Sands, G. B., Zhao, J., LeGrice, I. J., & Smaill, B. H. (2021). A novel system for mapping regional electrical properties and characterizing arrhythmia in isolated intact rat atria. American journal of physiology. Heart and circulatory physiology, 321(2), H412–H421. https://doi.org/10.1152/ajpheart.00185.2021

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RT-LAMP assays using in-house produced enzymes show promise for accurate and affordable SARS-CoV-2 testing

Alekseenko, A., Barrett, D., Pareja-Sanchez, Y. et al. Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples. Sci Rep 11, 1820 (2021). https://doi.org/10.1038/s41598-020-80352-8

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A sensitive EvaGreen-based PCR assay for measuring dNTP concentrations in cells and tissue

Purhonen, J., Banerjee, R., McDonald, A.E., Fellman, V., Kallijärvi, J., A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase. Nucleic Acids Research 48, e87 (2020). https://doi.org/10.1093/nar/gkaa516

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PICASSO: Ultra-multiplexed fluorescence imaging of biomolecules through single-round imaging and blind source unmixing

Seo, J., Sim, Y., Kim, J., Kim, H., Cho, I., Yoon, Y., & Chang, J.-B.(2022) PICASSO: Ultra-multiplexed fluorescence imaging of biomolecules through single-round imaging and blind source unmixing. Nat Commun 13, 2475. https://doi.org/10.1038/s41467-022-30168-z

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Exosome profiling with CF® dye tetraspanin panel shows single tetraspanin immunocapture methods may limit cancer biomarker detection

Mizenko, R. R., Brostoff, T., Rojalin, T., Koster, H. J., Swindell, H. S., Leiserowitz, G. S., … Carney, R. P. (2021). Tetraspanin immunocapture phenotypes extracellular vesicles according to biofluid source but may limit identification of multiplexed cancer biomarkers. BioRxiv, 2021.03.02.433595. https://doi.org/10.1101/2021.03.02.433595

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Spectrally distinct CF® Dyes enable a 43 color high dimensional spectral flow panel designed to characterize human peripheral blood mononuclear cells

Sahir F, Mateo JM, Steinhoff M, Siveen KS. Development of a 43 color panel for the characterization of conventional and unconventional T-cell subsets, B cells, NK cells, monocytes, dendritic cells, and innate lymphoid cells using spectral flow cytometry. Cytometry. 2020;1–7. https://doi.org/10.1002/cyto.a.24288

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Fast three-color single-molecule FRET using statistical inference

Yoo, J., Kim, JY., Louis, J.M. et al. Fast three-color single-molecule FRET using statistical inference. Nat Commun 11, 3336 (2020). https://doi.org/10.1038/s41467-020-17149-w Kim, JY and Chung, HS, Disordered Proteins Follow Diverse Transition Paths as They Fold and Bind to a Partner. Science 368, 1253 (2020) https://doi.org/10.1126/science.aba3854

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Measuring mitochondrial mass as an indicator of cellular health and functional autophagy

Zijian Tang, Kuo-Hui Su, Meng Xu, & Chengkai Dai (2020) HSF1 physically neutralizes amyloid oligomers to empower overgrowth and bestow neuroprotection. Science Advances https://doi.org/10.1126/sciadv.abc6871 Yang, G., Song, W., Xu, J. et al. (2020) Pik3c3 deficiency in myeloid cells imparts partial resistance to experimental autoimmune encephalomyelitis associated with reduced IL-1β production. Cell Mol Immunol. https://doi.org/10.1038/s41423-020-00589-1

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CF® Dyes light the way for high dimensional analysis by spectral flow cytometry

Jiang, J., Li, X., Mao, F., Wu, X., & Chen, Y. (2020). Small molecular fluorescence dyes for immuno cell analysis. Analytical Biochemistry, 114063. https://doi.org/10.1016/j.ab.2020.114063

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Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity

L. Cantuti-Castelvetri et al. (2020), Neuropilin-1 facilitates SARS-CoV-2 cell entry and infectivity Science https://doi.org/10.1126/science.abd2985

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Fast and multiplexed super-resolution imaging with DNA-PAINT-ERS

Civitci, F., Shangguan, J., Zheng, T., Tao, K., Rames, M., Kenison, J., Zhang, Y., Wu, L., Phelps, C., Esener, S., Nan, X. (2020). In Vivo Single-Molecule Detection of Nanoparticles for Multiphoton Fluorescence Correlation Spectroscopy to Quantify Cerebral Blood Flow. Nature Communications. https://doi.org/10.1038/s41467-020-18181-6

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Novel Method for Monitoring Cerebral Blood Flow with Subvessel Resolution In Vivo

Fu, X., Sompol, P., Brandon, J., Norris, C., Wilkop, T., Johnson, L., & Richards, C. (2020). In Vivo Single-Molecule Detection of Nanoparticles for Multiphoton Fluorescence Correlation Spectroscopy to Quantify Cerebral Blood Flow. Nano Letters. https://doi.org/10.1021/acs.nanolett.0c02280

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Sensitivity assessment of RT-qPCR and droplet digital PCR for SARS-CoV-2 detection

Falzone, L., Musso, N., Gattuso, G., Bongiorno, D., Palermo, C., Scalia, G., … Stefani, S. (2020). Sensitivity assessment of droplet digital PCR for SARS-CoV-2 detection. International Journal of Molecular Medicine, 46(3), 957–964. https://doi.org/10.3892/ijmm.2020.4673

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A pathologist’s guide for using expansion microscopy for nanoscale imaging of clinical specimens

Bucur O, Fu F, Calderon M, et al. 2020 Nat Protoc. 15(5):1649-1672. Nanoscale imaging of clinical specimens using conventional and rapid-expansion pathology. doi:10.1038/s41596-020-0300-1

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Microtubules as a Biomarker for Taxane Chemotherapy Response

Mukhtar, E., Worroll, D., Galletti, G., Schuster, S., Piha-Paul, S. A., &Giannakakou, P. (2020). Quantitative analysis of taxane drug target engagement of microtubules in circulating tumor cells from metastatic castration resistant prostate cancer patients treated with CRXL301, a nanoparticle of docetaxel. Cancer Drug Resistance.https://cdrjournal.com/article/view/3425

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Smartphone-Based Multiplex 30-minute Nucleic Acid Test of Live Virus from Nasal Swab Extract

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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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