@article{Park2025,

title = {Simple dual filter workflow for facilitating blood culture-free and sensitive detection of pathogenic bacteria from blood},

author = {D.J.M. Park, T. Wu, L. Chen, P.W. Lee, K. Hsieh and T.H. Wang},

doi = {https://doi.org/10.1038/s41598-025-08987-z},

year  = {2025},

date = {2025-07-09},

urldate = {2025-07-09},

journal = {Scientific Reports},

volume = {15},

number = {24766},

issue = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Park2025b,

title = {FlexPCR: A Streamlined Multiplexed Digital mRNA Quantification Platform with Universal Primers and Limited Fluorescence Channels},

author = {J.S. Park, J. Hu, L. Chen, and T.H. Wang},

url = {https://www.sciencedirect.com/science/article/pii/S0956566325001514},

doi = {https://doi.org/10.1016/j.bios.2025.117277},

year  = {2025},

date = {2025-06-01},

journal = {Biosensors and Bioelectronics},

volume = {277},

pages = {117277},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lee2025,

title = {Cross-Kingdom Pathogen Detection via Duplex Universal PCR and High-Resolution Melt},

author = {P.W. Lee, M. Totten, A. Traylor, S.X. Zhang, T.H. Wang and K. Hsieh},

url = {https://www.sciencedirect.com/science/article/pii/S0956566324009291},

doi = {https://doi.org/10.1016/j.bios.2024.116922},

year  = {2025},

date = {2025-02-15},

urldate = {2025-02-15},

journal = {Biosensors and Bioelectronics},

volume = {270},

number = {116922},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zhao2024,

title = {Multiplex digital profiling of DNA methylation heterogeneity for sensitive and cost-effective cancer detection in low-volume liquid biopsies},

author = {Y. Zhao, C.M. O’Keefe, J. Hu, C.M. Allan, W. Cui, H. Lei, A. Chiu, K. Hsieh, S.C. Joyce, J.G. Herman, T.R. Pisanic, T.H. Wang},

url = {https://www.science.org/doi/10.1126/sciadv.adp1704},

doi = {DOI: 10.1126/sciadv.adp1704},

year  = {2024},

date = {2024-11-22},

journal = {Science Advances},

volume = {10},

issue = {47},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hu2024,

title = {A streamlined proximity extension assay using POEGMA polymer-coated magnetic beads for enhanced protein detection},

author = {J. Hu, P. Zhang, F. Shao, T.H. Wang},

url = {https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2024.1462203/full},

doi = {https://doi.org/10.3389/fbioe.2024.1462203},

year  = {2024},

date = {2024-11-20},

journal = {Frontiers in Bioengineering and Biotechnology},

volume = {12},

number = {1462203},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hu2024b,

title = {Exploiting β‐Lactams‐Induced Lysis and DNA Fragmentation for Rapid Molecular Antimicrobial Susceptibility Testing of Neisseria Gonorrhoeae via Dual‐Digital PCR},

author = {J. Hu, L. Chen, P. Zhang, F.E. Chen, H. Li, K. Hsieh, S. Li, J.H. Melendez, T.H. Wang},

url = {https://advanced.onlinelibrary.wiley.com/doi/10.1002/advs.202405272?msockid=3d93250867086f4720e3334666846ee6},

doi = {https://doi.org/10.1002/advs.202405272},

year  = {2024},

date = {2024-10-18},

journal = {Advanced Science},

volume = {11},

number = {2405272},

issue = {46},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hu2024c,

title = {Supramolecular assembly of polycation/mRNA nanoparticles and in vivo monocyte programming},

author = {Y. Hu, S.Y. Tzeng, L. Cheng, J. Lin, A. Villabona-Rueda, S. Yu, S. Li, Z. Schneiderman, Y. Zhu, J. Ma, D.R. Wilson, S.R. Shannon, T. Warren, Y. Rui, C. Qiu, E.W. Kavanagh, K.M. Luly, Y. Zhang, N. Korinetz, F.R. D’Alessio, T.H. Wang, E. Kokkoli, S.K. Reddy, E. Luijten, J.J. Green, H.Q. Mao},

url = {https://pubmed.ncbi.nlm.nih.gov/39172792/},

doi = {DOI: 10.1073/pnas.2400194121},

year  = {2024},

date = {2024-08-22},

journal = {Proceedings of the National Academy of Sciences},

volume = {27},

number = {35},

issue = {121},

pages = {e2400194121},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{O'Keefe2024,

title = {Single-molecule epiallelic profiling of DNA derived from routinely collected Pap specimens for noninvasive detection of ovarian cancer},

author = {C.M. O'Keefe, Y. Zhao, L.M. Cope, C.M. Ho, A.N. Fader, R. Stone, J.S. Ferris, A. Beavis, K. Levinson, S. Wethington, T.L. Wang, T.R. Pisanic, I.M. Shih, T.H. Wang},

url = {https://onlinelibrary.wiley.com/doi/10.1002/ctm2.1778},

doi = {https://doi.org/10.1002/ctm2.1778},

year  = {2024},

date = {2024-07-31},

journal = {Clinical and Translational Medicine},

volume = {14},

issue = {8},

pages = {e1778},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Digitized Kinetic Analysis Enhances Genotyping Capacity of CRISPR-Based Biosensing},

author = {J.S. Park, P. Akarapipad, F.E. Chen, F. Shao, H. Mostafa, K. Hsieh, T.H. Wang},

url = {https://pubs.acs.org/doi/10.1021/acsnano.4c05312},

doi = {doi/10.1021/acsnano.4c05312.},

year  = {2024},

date = {2024-06-26},

journal = {ACS Nano},

volume = {18},

issue = {27},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ngo2024,

title = {Rapid and Portable Quantification of HIV RNA via a Smartphone-enabled Digital CRISPR Device and Deep Learning},

author = {H.T. Ngo, P. Akarapipad, P.W. Lee, J.S.Park, F.E. Chen, A.Y. Trick, K. Hsieh, T.H. Wang},

url = {https://www.sciencedirect.com/science/article/pii/S2666053924000286},

doi = {https://doi.org/10.1016/j.snr.2024.100212},

year  = {2024},

date = {2024-06-19},

journal = {Sensors and Actuators Reports},

volume = {8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Li2024,

title = {Single-Particle Spectroscopic Chromatography Reveals Heterogeneous RNA Loading and Size Correlations in Lipid Nanoparticles},

author = {S Li, Y Hu, J Lin, Z Schneiderman, F Shao, L Wei, A Li, K Hsieh, E Kokkoli, T. Curk, H.Q. Mao, T.H. Wang},

url = {https://pubs.acs.org/doi/full/10.1021/acsnano.4c02341},

doi = {doi/10.1021/acsnano.4c02341},

year  = {2024},

date = {2024-06-05},

journal = {ACS Nano},

volume = {18},

issue = {24},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hasnain2024,

title = {Cancer Methylation Biomarker Detection in an Automated, Portable, Multichannel Magnetofluidic Platform},

author = {A.C. Hasnain, A. Stark, A.Y. Trick, K. Ma, K. Hsieh, Y. Cheng, S.J. Meltzer, T.H. Wang},

url = {https://pubs.acs.org/doi/10.1021/acsnano.3c10070},

doi = {doi/10.1021/acsnano.3c10070},

year  = {2024},

date = {2024-04-26},

journal = {ACS Nano},

volume = {18},

issue = {19},

pages = {12105–12116},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Improving bacteria identification from digital melt assay via oligonucleotide-based temperature calibration},

author = {A. Traylor, P.W. Lee, K. Hsieh, T.H. Wang},

url = {https://www.sciencedirect.com/science/article/pii/S0003267024001727},

doi = {https://doi.org/10.1016/j.aca.2024.342371},

year  = {2024},

date = {2024-04-08},

journal = {Analytica Chimica Acta},

volume = {1297},

issue = {342371},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Shao2024,

title = {Automated and miniaturized screening of antibiotic combinations via robotic-printed combinatorial droplet platform},

author = {F. Shao, H. Li, K. Hsieh, P. Zhang, S. Li, T.H. Wang},

url = {https://www.sciencedirect.com/science/article/pii/S2211383523004501},

doi = {https://doi.org/10.1016/j.apsb.2023.11.027},

year  = {2024},

date = {2024-04-07},

journal = {Acta Pharmaceutica Sinica B},

volume = {14},

issue = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Khire2023,

title = {Rapid Minimum Inhibitory Concentration (MIC) Analysis Using Lyophilized Reagent Beads in a Novel Multiphase, Single-Vessel Assay},

author = {T. S. Khire, W. Gao, B. Bales, K. Hsieh, G. Grossmann, D.J.M. Park, C. O’Keefe, A. Brown-Countess, S. Peterson, F.E. Chen, R. Lenigk, A. Trick, T.H. Wang, C. Puleo},

url = {https://www.mdpi.com/2079-6382/12/11/1641},

doi = {https://doi.org/10.3390/antibiotics12111641},

year  = {2023},

date = {2023-11-19},

journal = {Antibiotics},

volume = {12},

issue = {11},

pages = {1641},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Harnessing Variabilities in Digital Melt Curves for Accurate Identification of Bacteria},

author = {P.W. Lee, L. Chen, K. Hsieh, A. Traylor, T.H. Wang},

url = {https://pubs.acs.org/doi/10.1021/acs.analchem.3c01654},

doi = {doi/10.1021/acs.analchem.3c01654},

year  = {2023},

date = {2023-10-09},

journal = {Analytical Chemistry},

volume = {95},

issue = {42},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Park2025,

title = {Simple dual filter workflow for facilitating blood culture-free and sensitive detection of pathogenic bacteria from blood},

author = {D.J.M. Park, T. Wu, L. Chen, P.W. Lee, K. Hsieh and T.H. Wang},

doi = {https://doi.org/10.1038/s41598-025-08987-z},

year  = {2025},

date = {2025-07-09},

urldate = {2025-07-09},

journal = {Scientific Reports},

volume = {15},

number = {24766},

issue = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Park2025b,

title = {FlexPCR: A Streamlined Multiplexed Digital mRNA Quantification Platform with Universal Primers and Limited Fluorescence Channels},

author = {J.S. Park, J. Hu, L. Chen, and T.H. Wang},

url = {https://www.sciencedirect.com/science/article/pii/S0956566325001514},

doi = {https://doi.org/10.1016/j.bios.2025.117277},

year  = {2025},

date = {2025-06-01},

journal = {Biosensors and Bioelectronics},

volume = {277},

pages = {117277},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lee2025,

title = {Cross-Kingdom Pathogen Detection via Duplex Universal PCR and High-Resolution Melt},

author = {P.W. Lee, M. Totten, A. Traylor, S.X. Zhang, T.H. Wang and K. Hsieh},

url = {https://www.sciencedirect.com/science/article/pii/S0956566324009291},

doi = {https://doi.org/10.1016/j.bios.2024.116922},

year  = {2025},

date = {2025-02-15},

urldate = {2025-02-15},

journal = {Biosensors and Bioelectronics},

volume = {270},

number = {116922},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zhao2024,

title = {Multiplex digital profiling of DNA methylation heterogeneity for sensitive and cost-effective cancer detection in low-volume liquid biopsies},

author = {Y. Zhao, C.M. O’Keefe, J. Hu, C.M. Allan, W. Cui, H. Lei, A. Chiu, K. Hsieh, S.C. Joyce, J.G. Herman, T.R. Pisanic, T.H. Wang},

url = {https://www.science.org/doi/10.1126/sciadv.adp1704},

doi = {DOI: 10.1126/sciadv.adp1704},

year  = {2024},

date = {2024-11-22},

journal = {Science Advances},

volume = {10},

issue = {47},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hu2024,

title = {A streamlined proximity extension assay using POEGMA polymer-coated magnetic beads for enhanced protein detection},

author = {J. Hu, P. Zhang, F. Shao, T.H. Wang},

url = {https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2024.1462203/full},

doi = {https://doi.org/10.3389/fbioe.2024.1462203},

year  = {2024},

date = {2024-11-20},

journal = {Frontiers in Bioengineering and Biotechnology},

volume = {12},

number = {1462203},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hu2024b,

title = {Exploiting β‐Lactams‐Induced Lysis and DNA Fragmentation for Rapid Molecular Antimicrobial Susceptibility Testing of Neisseria Gonorrhoeae via Dual‐Digital PCR},

author = {J. Hu, L. Chen, P. Zhang, F.E. Chen, H. Li, K. Hsieh, S. Li, J.H. Melendez, T.H. Wang},

url = {https://advanced.onlinelibrary.wiley.com/doi/10.1002/advs.202405272?msockid=3d93250867086f4720e3334666846ee6},

doi = {https://doi.org/10.1002/advs.202405272},

year  = {2024},

date = {2024-10-18},

journal = {Advanced Science},

volume = {11},

number = {2405272},

issue = {46},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hu2024c,

title = {Supramolecular assembly of polycation/mRNA nanoparticles and in vivo monocyte programming},

author = {Y. Hu, S.Y. Tzeng, L. Cheng, J. Lin, A. Villabona-Rueda, S. Yu, S. Li, Z. Schneiderman, Y. Zhu, J. Ma, D.R. Wilson, S.R. Shannon, T. Warren, Y. Rui, C. Qiu, E.W. Kavanagh, K.M. Luly, Y. Zhang, N. Korinetz, F.R. D’Alessio, T.H. Wang, E. Kokkoli, S.K. Reddy, E. Luijten, J.J. Green, H.Q. Mao},

url = {https://pubmed.ncbi.nlm.nih.gov/39172792/},

doi = {DOI: 10.1073/pnas.2400194121},

year  = {2024},

date = {2024-08-22},

journal = {Proceedings of the National Academy of Sciences},

volume = {27},

number = {35},

issue = {121},

pages = {e2400194121},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{O'Keefe2024,

title = {Single-molecule epiallelic profiling of DNA derived from routinely collected Pap specimens for noninvasive detection of ovarian cancer},

author = {C.M. O'Keefe, Y. Zhao, L.M. Cope, C.M. Ho, A.N. Fader, R. Stone, J.S. Ferris, A. Beavis, K. Levinson, S. Wethington, T.L. Wang, T.R. Pisanic, I.M. Shih, T.H. Wang},

url = {https://onlinelibrary.wiley.com/doi/10.1002/ctm2.1778},

doi = {https://doi.org/10.1002/ctm2.1778},

year  = {2024},

date = {2024-07-31},

journal = {Clinical and Translational Medicine},

volume = {14},

issue = {8},

pages = {e1778},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Digitized Kinetic Analysis Enhances Genotyping Capacity of CRISPR-Based Biosensing},

author = {J.S. Park, P. Akarapipad, F.E. Chen, F. Shao, H. Mostafa, K. Hsieh, T.H. Wang},

url = {https://pubs.acs.org/doi/10.1021/acsnano.4c05312},

doi = {doi/10.1021/acsnano.4c05312.},

year  = {2024},

date = {2024-06-26},

journal = {ACS Nano},

volume = {18},

issue = {27},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ngo2024,

title = {Rapid and Portable Quantification of HIV RNA via a Smartphone-enabled Digital CRISPR Device and Deep Learning},

author = {H.T. Ngo, P. Akarapipad, P.W. Lee, J.S.Park, F.E. Chen, A.Y. Trick, K. Hsieh, T.H. Wang},

url = {https://www.sciencedirect.com/science/article/pii/S2666053924000286},

doi = {https://doi.org/10.1016/j.snr.2024.100212},

year  = {2024},

date = {2024-06-19},

journal = {Sensors and Actuators Reports},

volume = {8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Li2024,

title = {Single-Particle Spectroscopic Chromatography Reveals Heterogeneous RNA Loading and Size Correlations in Lipid Nanoparticles},

author = {S Li, Y Hu, J Lin, Z Schneiderman, F Shao, L Wei, A Li, K Hsieh, E Kokkoli, T. Curk, H.Q. Mao, T.H. Wang},

url = {https://pubs.acs.org/doi/full/10.1021/acsnano.4c02341},

doi = {doi/10.1021/acsnano.4c02341},

year  = {2024},

date = {2024-06-05},

journal = {ACS Nano},

volume = {18},

issue = {24},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hasnain2024,

title = {Cancer Methylation Biomarker Detection in an Automated, Portable, Multichannel Magnetofluidic Platform},

author = {A.C. Hasnain, A. Stark, A.Y. Trick, K. Ma, K. Hsieh, Y. Cheng, S.J. Meltzer, T.H. Wang},

url = {https://pubs.acs.org/doi/10.1021/acsnano.3c10070},

doi = {doi/10.1021/acsnano.3c10070},

year  = {2024},

date = {2024-04-26},

journal = {ACS Nano},

volume = {18},

issue = {19},

pages = {12105–12116},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Improving bacteria identification from digital melt assay via oligonucleotide-based temperature calibration},

author = {A. Traylor, P.W. Lee, K. Hsieh, T.H. Wang},

url = {https://www.sciencedirect.com/science/article/pii/S0003267024001727},

doi = {https://doi.org/10.1016/j.aca.2024.342371},

year  = {2024},

date = {2024-04-08},

journal = {Analytica Chimica Acta},

volume = {1297},

issue = {342371},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Shao2024,

title = {Automated and miniaturized screening of antibiotic combinations via robotic-printed combinatorial droplet platform},

author = {F. Shao, H. Li, K. Hsieh, P. Zhang, S. Li, T.H. Wang},

url = {https://www.sciencedirect.com/science/article/pii/S2211383523004501},

doi = {https://doi.org/10.1016/j.apsb.2023.11.027},

year  = {2024},

date = {2024-04-07},

journal = {Acta Pharmaceutica Sinica B},

volume = {14},

issue = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Khire2023,

title = {Rapid Minimum Inhibitory Concentration (MIC) Analysis Using Lyophilized Reagent Beads in a Novel Multiphase, Single-Vessel Assay},

author = {T. S. Khire, W. Gao, B. Bales, K. Hsieh, G. Grossmann, D.J.M. Park, C. O’Keefe, A. Brown-Countess, S. Peterson, F.E. Chen, R. Lenigk, A. Trick, T.H. Wang, C. Puleo},

url = {https://www.mdpi.com/2079-6382/12/11/1641},

doi = {https://doi.org/10.3390/antibiotics12111641},

year  = {2023},

date = {2023-11-19},

journal = {Antibiotics},

volume = {12},

issue = {11},

pages = {1641},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Harnessing Variabilities in Digital Melt Curves for Accurate Identification of Bacteria},

author = {P.W. Lee, L. Chen, K. Hsieh, A. Traylor, T.H. Wang},

url = {https://pubs.acs.org/doi/10.1021/acs.analchem.3c01654},

doi = {doi/10.1021/acs.analchem.3c01654},

year  = {2023},

date = {2023-10-09},

journal = {Analytical Chemistry},

volume = {95},

issue = {42},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Tjandra2023,

title = {Rapid Molecular Phenotypic Antimicrobial Susceptibility Test for Neisseria gonorrhoeae Based on Propidium Monoazide Viability PCR},

author = {KC. Tjandra and N. Ram-Mohan and R. Abe and TH. Wang and S. Yang},

url = {https://pubmed.ncbi.nlm.nih.gov/37115656/},

doi = {doi: 10.1021/acsinfecdis.3c00096.},

year  = {2023},

date = {2023-05-12},

journal = {ACS Infectious Diseases},

volume = {9},

issue = {5},

pages = {1160-1167},

abstract = {Neisseria gonorrhoeae (NG) is an urgent threat to antimicrobial resistance (AMR) worldwide. NG has acquired rapid resistance to all previously recommended treatments, leaving ceftriaxone monotherapy as the first and last line of therapy for uncomplicated NG. The ability to rapidly determine susceptibility, which is currently nonexistent for NG, has been proposed as a strategy to preserve ceftriaxone by using alternative treatments. Herein, we used a DNA-intercalating dye in combination with NG-specific primers/probes to generate qPCR cycle threshold (Ct) values at different concentrations of 2 NG-relevant antimicrobials. Our proof-of-concept dual-antimicrobial logistic regression model based on the differential Ct measurements achieved an AUC of 0.93 with a categorical agreement for the susceptibility of 84.6%. When surveying the performance against each antimicrobial separately, the model predicted 90 and 75% susceptible and resistant strains, respectively, to ceftriaxone and 66.7 and 83.3% susceptible and resistant strains, respectively, to ciprofloxacin. We further validated the model against the individual replicates and determined the accuracy of the model in classifying susceptibility agnostic of the inoculum size. We demonstrated a novel PCR-based approach to determine phenotypic ciprofloxacin and ceftriaxone susceptibility information for NG with reasonable accuracy within 30 min, a significant improvement compared to the conventional method which could take multiple days.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chen2023,

title = {Point-of-Care Amenable Detection of Mycoplasma genitalium and Its Antibiotic Resistance Mutations},

author = {F. Chen and J. Wang and AH. Nambiar and J. Hardick and J. Melendez and AY. Trick and TH. Wang},

url = {https://pubmed.ncbi.nlm.nih.gov/36961769/},

doi = {DOI: 10.1021/acssensors.2c02630},

year  = {2023},

date = {2023-04-28},

journal = {ACS Sensors},

volume = {8},

issue = {4},

pages = {1550-1557},

abstract = {Mycoplasma genitalium (MG) is an emerging sexually transmitted bacterium. Due to its fastidious and slow-growing nature, MG is difficult to detect through culture-based diagnostics. Like Neisseria gonorrheae, another bacterial pathogen linked to sexually transmitted infections (STIs), MG has developed resistance to macrolide and fluoroquinolone antibiotics used to treat STIs. The ability to detect MG and identify genomic mutations associated with antibiotic resistance simultaneously can enable antibiotic stewardship and mitigate the spread of antibiotic-resistant MG. Toward this end, we first developed a multiplexed probe-based PCR-melt assay that detects MG and the presence of macrolide resistance mutations in the 23S rRNA gene and fluoroquinolone resistance mutations in the parC gene. Each target was identified via its unique combination of fluorescence label and melting temperature. This approach allowed differentiation between the different types of mutations at the genes of interest. Following initial assay optimization, the assay was integrated into a droplet magnetofluidic cartridge used in a portable platform to integrate automated sample extraction, PCR amplification, and detection. Lastly, we demonstrated that the integrated assay and droplet magnetofluidic platform could detect MG and antibiotic resistance-associated mutations in clinical isolates spiked into urine samples in 40 min.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zhao2023,

title = {Multiplex Digital Methylation‐Specific PCR for Noninvasive Screening of Lung Cancer},

author = {Y. Zhao and CM. O'Keefe and K. Hsieh and L. Cope and SC. Joyce and TR. Pisanic and JG. Herman and TH. Wang },

url = {https://pubmed.ncbi.nlm.nih.gov/37039321/},

year  = {2023},

date = {2023-04-11},

journal = {Advanced Science},

volume = {e2206518},

abstract = {There remains tremendous interest in developing liquid biopsy assays for detection of cancer-specific alterations, such as mutations and DNA methylation, in cell-free DNA (cfDNA) obtained through noninvasive blood draws. However, liquid biopsy analysis is often challenging due to exceedingly low fractions of circulating tumor DNA (ctDNA), necessitating the use of extended tumor biomarker panels. While multiplexed PCR strategies provide advantages such as higher throughput, their implementation is often hindered by challenges such as primer-dimers and PCR competition. Alternatively, digital PCR (dPCR) approaches generally offer superior performance, but with constrained multiplexing capability. This paper describes development and validation of the first multiplex digital methylation-specific PCR (mdMSP) platform for simultaneous analysis of four methylation biomarkers for liquid-biopsy-based detection of non-small cell lung cancer (NSCLC). mdMSP employs a microfluidic device containing four independent, but identical modules, housing a total of 40 160 nanowells. Analytical validation of the mdMSP platform demonstrates multiplex detection at analytical specificities as low as 0.0005%. The clinical utility of mdMSP is also demonstrated in a cohort of 72 clinical samples of low-volume liquid biopsy specimens from patients with computed tomography (CT)-scan indeterminant pulmonary nodules, exhibiting superior clinical performance when compared to traditional MSP assays for noninvasive detection of early-stage NSCLC.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chen2023b,

title = {Point-of-Care Amenable Detection of Mycoplasma genitalium and Its Antibiotic Resistance Mutations},

author = {F.E. Chen, J. Wang, A.H. Nambiar, J. Hardick, J. Melendez, A.Y. Trick, T.H. Wang},

url = {https://pubs.acs.org/doi/10.1021/acssensors.2c02630},

doi = {doi/10.1021/acssensors.2c02630},

year  = {2023},

date = {2023-03-24},

journal = {ACS Sensors},

volume = {8},

issue = {4},

pages = {1550-1557},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zhu2023b,

title = {Dectin-1 signaling on colonic γδ T cells promotes psychosocial stress responses},

author = {X. Zhu, S. Sakamoto, C. Ishii, M.D. Smith, Koki Ito, M. Obayashi, L. Unger, Y. Hasegawa, S. Kurokawa, T. Kishimoto, H. L, S. Hatano, T.H. Wang, Y. Yoshikai, S. Kano, S. Fukuda, K. Sanada1, P.A. Calabresi, A. Kamiya},

url = {https://www.nature.com/articles/s41590-023-01447-8},

doi = {https://doi.org/10.1038/s41590-023-01447-8},

year  = {2023},

date = {2023-03-20},

journal = {Nature Immunology},

volume = {24},

number = {625–636},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zhu2023,

title = {Dectin-1 signaling on colonic γδ T cells promotes psychosocial stress responses},

author = {X. Zhu and S. Sakamoto and C. Ishii and MD. Smith and K. Ito and M. Obayashi and L. Unger and Y. Hasegawa and S. Kurokawa and T. Kishimoto and H. Li and S. Hatano and TH. Wang and Y. Yoshikai and S. Kano and S. Fukuda and K. Sanada and PA. Calabresi and A. Kamiya

},

url = {https://pubmed.ncbi.nlm.nih.gov/36941398/},

doi = {DOI: 10.1038/s41590-023-01447-8},

year  = {2023},

date = {2023-03-20},

journal = {Nature Immunology},

volume = {24},

pages = {625-636},

abstract = {The intestinal immune system interacts with commensal microbiota to maintain gut homeostasis. Furthermore, stress alters the microbiome composition, leading to impaired brain function; yet how the intestinal immune system mediates these effects remains elusive. Here we report that colonic γδ T cells modulate behavioral vulnerability to chronic social stress via dectin-1 signaling. We show that reduction in specific Lactobacillus species, which are involved in T cell differentiation to protect the host immune system, contributes to stress-induced social-avoidance behavior, consistent with our observations in patients with depression. Stress-susceptible behaviors derive from increased differentiation in colonic interleukin (IL)-17-producing γδ T cells (γδ17 T cells) and their meningeal accumulation. These stress-susceptible cellular and behavioral phenotypes are causally mediated by dectin-1, an innate immune receptor expressed in γδ T cells. Our results highlight the previously unrecognized role of intestinal γδ17 T cells in the modulation of psychological stress responses and the importance of dectin-1 as a potential therapeutic target for the treatment of stress-induced behaviors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Shao2023,

title = {Elucidating the Role of CRISPR/Cas in Single-Step Isothermal Nucle-ic Acid Amplification Testing Assays},

author = {F. Shao and JS. Park and G. Zhao, and K. Hsieh and TH. Wang},

url = {https://pubmed.ncbi.nlm.nih.gov/36745596/},

doi = {DOI: 10.1021/acs.analchem.2c05632},

year  = {2023},

date = {2023-02-21},

journal = {Analytical Chemistry},

volume = {95},

issue = {7},

pages = {3873-3882},

abstract = {Developing assays that combine CRISPR/Cas and isothermal nucleic acid amplification has become a burgeoning research area due to the novelty and simplicity of CRISPR/Cas and the potential for point-of-care uses. Most current research explores various two-step assays by appending different CRISPR/Cas effectors to the end of different isothermal nucleic acid amplification methods. However, efforts in integrating both components into more ideal single-step assays are scarce, and poor-performing single-step assays have been reported. Moreover, lack of investigations into CRISPR/Cas in single-step assays results in incomplete understanding. To fill this knowledge gap, we conducted a systematic investigation by developing and comparing assays that share the identical recombinase polymerase amplification (RPA) but differ in CRISPR/Cas12a. We found that the addition of CRISPR/Cas12a indeed unlocks signal amplification but, at the same time, impedes RPA and that CRISPR/Cas12a concentration is a key parameter for attenuating RPA impediment and ensuring assay performance. Accordingly, we found that our protospacer adjacent motif (PAM)-free CRISPR/Cas12a-assisted RPA assay, which only moderately impeded RPA at its optimal CRISPR/Cas12a concentration, outperformed its counterparts in assay design, signal, sensitivity, and speed. We also discovered that a new commercial Cas12a effector could also drive our PAM-free CRISPR/Cas12a-assisted RPA assay and reduce its cost, though simultaneously lowering its signal. Our study and the new insights can be broadly applied to steer and facilitate further advances in CRISPR/Cas-based assays.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Shao2023b,

title = {Elucidating the Role of CRISPR/Cas in Single-Step Isothermal Nucleic Acid Amplification Testing Assays},

author = {F. Shao, J. S. Park, G. Zhao, K. Hsieh, T.H. Wang},

url = {https://pubs.acs.org/doi/10.1021/acs.analchem.2c05632},

doi = {doi/10.1021/acs.analchem.2c05632.},

year  = {2023},

date = {2023-02-06},

journal = {Analytical Chemistry},

volume = {95},

issue = {7},

pages = {3873-3882},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Li2023,

title = {Single-cell pathogen diagnostics for combating antibiotic resistance},

author = {H. Li and K. Hsieh and P. Wong and K. Mach and J. Liao and TH. Wang},

url = {https://www.nature.com/articles/s43586-023-00201-6},

doi = {DOI: 10.1021/acs.accounts.1c00462},

year  = {2023},

date = {2023-02-02},

journal = {Nature Reviews Methods Primers},

volume = {3},

number = {6},

issue = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Li2023b,

title = {Single-cell pathogen diagnostics for combating antibiotic resistance},

author = {H. Li, K. Hsieh, P. Wong, K. Mach, J. Liao, T.H, Wang},

url = {https://www.nature.com/articles/s43586-022-00190-y},

doi = {DOI: 10.1038/s43586-022-00190-y},

year  = {2023},

date = {2023-02-02},

journal = {Nature Reviews Methods Primers},

volume = {95},

issue = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ngo2023b,

title = {Sensitive and Quantitative Point-of-Care HIV Viral Load Quantification from Blood Using a Power-Free Plasma Separation and Portable Magnetofluidic Polymerase Chain Reaction Instrument},

author = {HT. Ngo and M. Jin and AY. Trick and FE. Chen and L. Chen and K. Hsieh and TH. Wang

},

url = {https://pubmed.ncbi.nlm.nih.gov/36562405/},

doi = {DOI: 10.1021/acs.analchem.2c03897},

year  = {2023},

date = {2023-01-17},

journal = { Analytical Chemistry},

volume = {95},

issue = {2},

pages = {1159–1168},

abstract = {Point-of-care (POC) HIV viral load (VL) tests are needed to enhance access to HIV VL testing in low- and middle-income countries (LMICs) and to enable HIV VL self-testing at home, which in turn have the potential to enhance the global management of the disease. While methods based on real-time reverse transcription-polymerase chain reaction (RT-PCR) are highly sensitive and quantitatively accurate, they often require bulky and expensive instruments, making applications at the POC challenging. On the other hand, although methods based on isothermal amplification techniques could be performed using low-cost instruments, they have shown limited quantitative accuracies, i.e., being only semiquantitative. Herein, we present a sensitive and quantitative POC HIV VL quantification method from blood that can be performed using a small power-free three-dimensional-printed plasma separation device and a portable, low-cost magnetofluidic real-time RT-PCR instrument. The plasma separation device, which is composed of a plasma separation membrane and an absorbent material, demonstrated 96% plasma separation efficiency per 100 μL of whole blood. The plasma solution was then processed in a magnetofluidic cartridge for automated HIV RNA extraction and quantification using the portable instrument, which completed 50 cycles of PCR in 15 min. Using the method, we achieved a limit of detection of 500 HIV RNA copies/mL, which is below the World Health Organization's virological failure threshold, and a good quantitative accuracy. The method has the potential for sensitive and quantitative HIV VL testing at the POC and at home self-testing.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ngo2022,

title = {Sensitive and Quantitative Point-of-Care HIV Viral Load Quantification from Blood Using a Power-Free Plasma Separation and Portable Magnetofluidic Polymerase Chain Reaction Instrument},

author = {H. T. Ngo, M. Jin, A.Y. Trick, F.E. Chen, L. Chen, K. Hsieh, T.H. Wang},

url = {https://pubs.acs.org/doi/full/10.1021/acs.analchem.2c03897},

doi = {doi/10.1021/acs.analchem.2c03897.},

year  = {2022},

date = {2022-12-23},

journal = {Analytical Chemistry},

volume = {9},

issue = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Akarapipad2022,

title = {Emerging Multiplex Nucleic Acid Diagnostic Tests for Combating COVID-19},

author = {P. Akarapipad and E. Bertelson and A. Pessell and TH. Wang and K. Hsieh

},

url = {https://pubmed.ncbi.nlm.nih.gov/36354487/},

doi = {DOI: 10.3390/bios12110978},

year  = {2022},

date = {2022-11-07},

urldate = {2022-11-07},

journal = {Biosensors},

volume = {12},

issue = {11},

pages = {978},

abstract = {The COVID-19 pandemic caused by SARS-CoV-2 has drawn attention to the need for fast and accurate diagnostic testing. Concerns from emerging SARS-CoV-2 variants and other circulating respiratory viral pathogens further underscore the importance of expanding diagnostic testing to multiplex detection, as single-plex diagnostic testing may fail to detect emerging variants and other viruses, while sequencing can be too slow and too expensive as a diagnostic tool. As a result, there have been significant advances in multiplex nucleic-acid-based virus diagnostic testing, creating a need for a timely review. This review first introduces frequent nucleic acid targets for multiplex virus diagnostic tests, then proceeds to a comprehensive and up-to-date overview of multiplex assays that incorporate various detection reactions and readout modalities. The performances, advantages, and disadvantages of these assays are discussed, followed by highlights of platforms that are amenable for point-of-care use. Finally, this review points out the remaining technical challenges and shares perspectives on future research and development. By examining the state of the art and synthesizing existing development in multiplex nucleic acid diagnostic tests, this review can provide a useful resource for facilitating future research and ultimately combating COVID-19.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Li2022,

title = {Payload distribution and capacity of mRNA lipid nanoparticles},

author = {S. Li and Y. Hu and A. Li and J. Lin and K. Hsieh and Z. Schneiderman and P. Zhang and Y. Zhu and C. Qiu and E. Kokkoli and TH. Wang and HQ. Mao},

doi = {https://doi.org/10.1038/s41467-022-33157-4},

year  = {2022},

date = {2022-09-23},

journal = {nature communications},

volume = {13},

number = {5561},

abstract = {Lipid nanoparticles (LNPs) are effective vehicles to deliver mRNA vaccines and therapeutics. It has been challenging to assess mRNA packaging characteristics in LNPs, including payload distribution and capacity, which are critical to understanding structure-property-function relationships for further carrier development. Here, we report a method based on the multi-laser cylindrical illumination confocal spectroscopy (CICS) technique to examine mRNA and lipid contents in LNP formulations at the single-nanoparticle level. By differentiating unencapsulated mRNAs, empty LNPs and mRNA-loaded LNPs via coincidence analysis of fluorescent tags on different LNP components, and quantitatively resolving single-mRNA fluorescence, we reveal that a commonly referenced benchmark formulation using DLin-MC3 as the ionizable lipid contains mostly 2 mRNAs per loaded LNP with a presence of 40%–80% empty LNPs depending on the assembly conditions. Systematic analysis of different formulations with control variables reveals a kinetically controlled assembly mechanism that governs the payload distribution and capacity in LNPs. These results form the foundation for a holistic understanding of the molecular assembly of mRNA LNPs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zhang2022,

title = {Highly Sensitive Serum Protein Analysis Using Magnetic Bead-Based Proximity Extension Assay},

author = {P. Zhang and J. Hu and JS. Park and K. Hsieh and L. Chen and A. Mao and TH. Wang},

url = {https://pubs.acs.org/doi/full/10.1021/acs.analchem.2c02684},

doi = {https://doi.org/10.1021/acs.analchem.2c02684},

year  = {2022},

date = {2022-08-30},

urldate = {2022-08-30},

journal = {Analytical Chemistry},

volume = {94},

issue = {36},

pages = {1281-12489},

abstract = {Many protein biomarkers are present in biofluids at a very low level but may play critical roles in important biological processes. The fact that these low-abundance proteins remain largely unexplored underscores the importance of developing new tools for highly sensitive protein detection. Although digital enzyme-linked immunosorbent assay (ELISA) has demonstrated ultrahigh sensitivity compared with conventional ELISA, the requirement of specialized instruments limits the accessibility and prevents the widespread implementation. On the other hand, proximity ligation assays (PLA) and proximity extension assays (PEA) show sensitive and specific protein detection using regular laboratory setups, but their sensitivity needs to be further improved to match digital ELISA. To achieve highly sensitive protein detection with minimal accessibility limitation, we develop a magnetic bead-based PEA (magPEA), which posts triple epitope recognition requirement and enables extensive washing for improved sensitivity and enhanced specificity. We demonstrate that the incorporation of magnetic beads into PEA workflow facilitates orders of magnitude sensitivity improvement compared with conventional ELISA, homogeneous PEA, and solid-phase PLA and achieves limits of detection close to that of digital ELISA when using IL-6, IL-8, and GM-CSF as validation. Our magPEA provides a simple approach for highly sensitive protein detection that can be readily implemented to other laboratories and will thus ultimately accelerate the study of the low abundance protein biomarkers in the future.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Facile and scalable tubing-free sample loading for droplet microfluidics},

author = {F. Shao and K. Hsieh and P. Zhang and AM. Kaushik and TH. Wang},

url = {https://www.nature.com/articles/s41598-022-17352-3},

doi = {https://doi.org/10.1038/s41598-022-17352-3},

year  = {2022},

date = {2022-08-03},

journal = {Scientific Reports},

volume = {12},

number = {13340},

issue = {1},

pages = {1-12},

abstract = {Droplet microfluidics has in recent years found a wide range of analytical and bioanalytical applications. In droplet microfluidics, the samples that are discretized into droplets within the devices are predominantly loaded through tubings, but such tubing-based sample loading has drawbacks such as limited scalability for processing many samples, difficulty for automation, and sample wastage. While advances in autosamplers have alleviated some of these drawbacks, sample loading that can instead obviate tubings offers a potentially promising alternative but has been underexplored. To fill the gap, we introduce herein a droplet device that features a new Tubing Eliminated Sample Loading Interface (TESLI). TESLI integrates a network of programmable pneumatic microvalves that regulate vacuum and pressure sources so that successive sub-microliter samples can be directly spotted onto the open-to-atmosphere TESLI inlet, vacuumed into the device, and pressurized into nanoliter droplets within the device with minimal wastage. The same vacuum and pressure regulation also endows TESLI with cleaning and sample switching capabilities, thus enabling scalable processing of many samples in succession. Moreover, we implement a pair of TESLIs in our device to parallelize and alternate their operation as means to minimizing idle time. For demonstration, we use our device to successively process 44 samples into droplets—a number that can further scale. Our results demonstrate the feasibility of tubing-free sample loading and a promising approach for advancing droplet microfluidics.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ma2022,

title = {Accurate Nonendoscopic Detection of Esophageal Squamous Cell Carcinoma Using Methylated DNA Biomarkers},

author = {K. Ma and A. Kalra and HL. Tsai and S. Okello and Y. Cheng and SJ. Meltzer and Esophagea Squamous Cell Carcinoma Consortium

},

url = {https://pubmed.ncbi.nlm.nih.gov/35483446/},

doi = {DOI: 10.1053/j.gastro.2022.04.021},

year  = {2022},

date = {2022-08-01},

journal = {Gastroenterology},

volume = { 163},

issue = {2},

pages = {507-509},

abstract = {Esophageal cancer, with 544,076 deaths in 2020, 1 includes esophageal adenocarcinoma and esophageal squamous cell carcinoma (ESCC). ESCC comprises 90% of esophageal cancers globally. The 5-year survival rate remains poor (15%–25% worldwide) because patients usually present with late disease. 2 Although ESCC can be diagnosed by means of esophagogastroduodenoscopy (EGD) with biopsy, EGD is not widely available in low-income countries. 2 Inexpensive, safe, accessible diagnostic alternatives will likely improve diagnosis and outcome.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Shao2022b,

title = {Emerging platforms for high-throughput enzymatic bioassays},

author = {F. Shao and P. Lee and H. Li and K. Hsieh and TH. Wang

},

url = {https://pubmed.ncbi.nlm.nih.gov/35863950/},

doi = {DOI: 10.1016/j.tibtech.2022.06.006},

year  = {2022},

date = {2022-07-18},

journal = {Trends in Biotechnology},

volume = { 41},

issue = {1},

pages = {120-133},

abstract = {Enzymes have essential roles in catalyzing biological reactions and maintaining metabolic systems. Many in vitro enzymatic bioassays have been developed for use in industrial and research fields, such as cell biology, enzyme engineering, drug screening, and biofuel production. Of note, many of these require the use of high-throughput platforms. Although the microtiter plate remains the standard for high-throughput enzymatic bioassays, microfluidic arrays and droplet microfluidics represent emerging methods. Each has seen significant advances and offers distinct advantages; however, drawbacks in key performance metrics, including reagent consumption, reaction manipulation, reaction recovery, real-time measurement, concentration gradient range, and multiplexity, remain. Herein, we compare recent high-throughput platforms using the aforementioned metrics as criteria and provide insights into remaining challenges and future research trends.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chen2022,

title = {Ratiometric PCR in a Portable Sample-to-Result Device for Broad-Based Pathogen Identification},

author = {FE. Chen and AY. Trick and AC. Hasnain and K. Hsieh and L. Chen and DJ. Shin and TH. Wang},

url = {https://pubs.acs.org/doi/full/10.1021/acs.analchem.2c01357},

doi = {https://doi.org/10.1021/acs.analchem.2c01357},

year  = {2022},

date = {2022-06-21},

urldate = {2022-06-21},

journal = {Analytical Chemistry},

volume = {94},

issue = {26},

pages = {9372-9379},

abstract = {Polymerase chain reaction (PCR)-based diagnostic testing is the gold standard method for pathogen identification (ID) with recent developments enabling automated PCR tests for point-of-care (POC) use. However, multiplexed identification of several pathogens in PCR assays typically requires optics for an equivalent number of fluorescence channels, increasing instrumentation’s complexity and cost. In this study, we first developed ratiometric PCR that surpassed one target per color barrier to allow multiplexed identification while minimizing optical components for affordable POC use. We realized it by amplifying pathogenic targets with fluorescently labeled hydrolysis probes with a specific ratio of red-to-green fluorophores for each bacterial species. We then coupled ratiometric PCR and automated magnetic beads-based sample preparation within a thermoplastic cartridge and a portable droplet magnetofluidic platform. We named the integrated workflow POC-ratioPCR. We demonstrated that the POC-ratioPCR could detect one out of six bacterial targets related to urinary tract infections (UTIs) in a single reaction using only two-color channels. We further evaluated POC-ratioPCR using mock bacterial urine samples spiked with good agreement. The POC-ratioPCR presents a simple and effective method for enabling broad-based POC PCR identification of pathogens directly from crude biosamples with low optical instrumentation complexity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}