Publications

2023

1. Assessing Breast Cancer Molecular Subtypes Using Extracellular Vesicles’ mRNA. Hu, Mengjia; Brown, Virginia; Jackson, Joshua; Wijerathne, Harshani; Pathak, Harsh; Koestler, Devin; Nissen, Emily; Hupert, Mateusz; Muller, Rolf; Godwin, Andrew K.; Witek, Malgorzata; Soper, Steven A.,
   Analytical Chemistry. 2023
   doi. 10.1021/acs.analchem.3c00624
   PMCID: 
2. Simple Micromilled Microfluidic Impedance Cytometer with Vertical Parallel Electrodes for Cell Viability Analysis. Micromachines, Eades, J.; Audiffred, J.F.; Fincher, M.; Choi, J.-W.; Soper, S.A.; Monroe, W.T. A .  
   MDPI. 2023
   doi. 10.3390/mi14020283
   PMCID: 
3. Nano-Coulter Counter for Detection of Exosomes and Viral Particles, Sachindra S. T. Gamage, Uditha S. Athapattu, Zheng Zhao, Junseo Choi, Sunggook Park, Malgorzata A. Witek, Collin McKinney, Matthew Verber, and Steven A. Soper, Swarnagowri Vaidyanathan,
   Analytical Chemistry. 2023, accepted
   doi. 
   PMCID: 

2022

1. Fluidic operation of a polymer-based nanosensor chip for analysing single molecules. Vaidyanathan S, Gamage S, Dathathreya K, Kryk R, Manoharan A, Zhao Z, Zhang L, Choi J, Park D, Park S, Soper SA.
   Flow (Camb). 2022; 2:E14.
   doi: 10.1017/flo.2022.8.
   PMCID: PMC9356744.
2. In-plane Extended Nano-coulter Counter (XnCC) for the Label-free Electrical Detection of Biological Particles
   Zheng Z., Swarnagowri V., Payel B., Gamage S., Subhrajit S., McKinney C., Choi J., Park S., Pahattuge T., Wijerathne H., Jackson JM., Hupert ML., Witek MA, Soper SA
   Electroanalysis. 2022 Jun 14
   doi: 10.1002/elan.202200091
   PMCID:
3. Microfluidic affinity selection of active SARS-CoV-2 virus particles.
   Gamage SST, Pahattuge TN, Wijerathne H, Childers K, Vaidyanathan S, Athapattu US, Zhang L, Zhao Z, Hupert ML, Muller RM, Muller-Cohn J, Dickerson J, Dufek D, Geisbrecht BV, Pathak H, Pessetto Z, Gan GN, Choi J, Park S, Godwin AK, Witek MA, Soper SA.
   Sci Adv. 2022  Sep 30
   doi: 10.1126/sciadv.abn9665.
   PMCID: PMC9519043
4. Modifying surface charge density of thermoplastic nanofluidic biosensors by multivalent cations within the slip plane of the electric double layer,
   Zheng Jia, Junseo Choi, Sunggun Lee, Steven A. Soper, Sunggook Park,
   Colloids and Surfaces A: Physicochemical and Engineering Aspects,
   Volume 648, 2022,
   Doi: 10.1016/j.colsurfa.2022.129147.
   PMCID: PMC9853209
5. Nanofluidic devices for the separation of biomolecules,
   Chathurika Rathnayaka, Charuni A. Amarasekara, Khurshed Akabirov, Michael C. Murphy, Sunggook Park, Malgorzata A. Witek, Steven A. Soper,
   Journal of Chromatography A, Volume 1683, 2022,
   Doi: 10.1016/j.chroma.2022.463539.
   PMCID: PMC9795076

2021

1. Tailoring Thermoplastic In-Plane Nanopore Size by Thermal Fusion Bonding for the Analysis of Single Molecules.
   Atapatt US, Rathnayaka C, Vaidyanathan S, Gamage SST, Choi J, Riahipour R, Manoharan A, Hall AR, Park S, Soper SA.
   ACS Sens. 2021 Aug 27; 6(8):3133-3143.
   doi: 10.1021/acssensors.1c01359.
   PMCID: PMC8482307.
2. System Modularity Chip for Analysis of Rare Targets (SMART-Chip): Liquid Biopsy Samples.
   Pahattuge TN, Freed IM, Hupert ML, Vaidyanathan S, Childers K, Witek MA, Weerakoon-Ratnayake K, Park D, Kasi A, Al-Kasspooles MF, Murphy MC, Soper SA.
   ACS Sens. 2021 May 28; 6(5):1831-1839.
   doi: 10.1021/acssensors.0c02728.
   PMCID: PMC8325110.
3. Thermoplastic nanofluidic devices for identifying abasic sites in single DNA molecules.
   Vaidyanathan S, Weerakoon-Ratnayake KM, Uba FI, Hu B, Kaufman D, Choi J, Park S, Soper SA.
   Lab Chip. 2021 Apr 20; 21(8):1579-1589.
   doi: 10.1039/d0lc01038c.
   PMCID: PMC8293902.
4. Solid-phase XRN1 reactions for RNA cleavage: application in single-molecule sequencing.
   Athapattu US, Amarasekara CA, Immel JR, Bloom S, Barany F, Nagel AC, Soper SA. Nucleic Acids Res. 2021 Apr 19; 49(7):e41.
   doi: 10.1093/nar/gkab001.
   PMCID: PMC8053086.
5. Electrokinetic identification of ribonucleotide monophosphates (rNMPs) using thermoplastic nanochannels.
   Amarasekara CA, Rathnayaka C, Athapattu US, Zhang L, Choi J, Park S, Nagel AC, Soper SA.
   J Chromatogr A. 2021 Feb 8;
   doi: 10.1016/j.chroma.2021.461892.
   PMCID: PMC8107831.
6. Flexible-templated imprinting for fluorine-free, omniphobic plastics with re-entrant structures.
   Zhao X, Park DS, Choi J, Park S, Soper SA, Murphy MC.
   J Colloid Interface Sci. 2021 Mar; 585:668-675.
    doi: 10.1016/j.jcis.2020.10.046.
   PMCID: PMC8483707.
7. Isolation and analysis methods of extracellular vesicles (EVs). Extracell VesiclesZhao Z, Wijerathne H, Godwin AK, Soper SA.
   Circ Nucl Acids. 2021; 2:80-103.
   doi: 10.20517/evcna.2021.07.
   PMCID: PMC8372011.
8. Label-Free Identification of Single Mononucleotides by Nanoscale Electrophoresis.
   Choi J, Jia Z, Riahipour R, McKinney CJ, Amarasekara CA, Weerakoon-Ratnayake KM, Soper SA, Park S.
   Small. 2021 Oct; 17(42):e2102567.
   doi: 10.1002/smll.202102567.
   PMCID: PMC8542607.
9. Analytical Technologies for Liquid Biopsy of Subcellular Materials.
   Campos CDM, Childers K, Gamage SST, Wijerathne H, Zhao Z, Soper SA.
   Annu Rev Anal Chem (Palo Alto Calif). 2021 Jul 27; 14(1):207-229.
   PMCID: PMC8601690.
10. Leakage pressures for gasketless superhydrophobic fluid interconnects for modular lab-on-a-chip systems.
    Brown CR, Zhao X, Park T, Chen PC, You BH, Park DS, Soper SA, Baird A, Murphy MC. Microsyst Nanoeng. 2021 Sep 2; 7:69.
    doi: 10.1038/s41378-021-00287-6.
    PMCID: PMC8433346.

2020

1. Cell Separations and Sorting
   MA Witek, IM Freed, SA Soper
   Analytical Chemistry, 2020, 92, 1, 105-131.
   DOI: 10.1021/acs.analchem.9b05357
   PMCID: PMC7469080
2. Prediction of Blood-Based Biomarkers and Subsequent Design of Bisulfite PCR-LDR-qPCR Assay for Breast Cancer Detection
   MD Bacolod, J Huang, SF Giardina, PB Feinberg, AH Mirza, A Swistel, SA Soper, F Barany
   BMC Cancer, 20:85 (2020)
   DOI: 10.1186/s12885-020-6574-4
   PMCID: PMC6995062
3. Label-free counting of affinity-enriched circulating tumor cells (CTCs) using a thermoplastic micro-Coulter counter (μCC)
   C Kong, M Hu, KM Weerakoon-Ratnayake, MA Witek, K Dathathreya, ML Hupert, SA Soper
   Analyst, 145 (5):1677-1696, 2020
   DOI: 10.1039/c9an01802f
   PMCID: PMC7350181
4. Visible Photorelease of Liquid Biopsy Markers Following Microfluidic Affinity-Enrichment
   TN Pahattuge, JM Jackson, R Digamber, H Wijerathne, V Brown, MA Witek, C Perera, RS Givens, BR Peterson, SA Soper
   Chemical Communications, 2020, 56, 4098-4101.
   DOI: 10.1039/C9CC09598E
   PMCID: PMC7469076
5. Microfluidic Device for On-Chip Immunophenotyping and Cytogenic Analysis of Rare Biological Cells
   KM Weerakoon-Ratnayake, S Vaidyanathan, N Larkey, K Dathathreya, M Hu, J Jose, S Mog, KJ August, AK Godwin, ML Hupert, MA Witek, SA Soper
   Cells, 2020 Feb 24; 9(2): 519.
   DOI: 10.3390/cells9020519
   PMCID: PMC7072755
6. Single-Molecule Detection of Cancer Mutations Using a Novel PCR-LDR-qPCR Assay
   C Ruiz, J Huang, SF Giardina, PB Feinberg, AH Mirza, MD Bacolod, SA Soper, F Barany
   Human Mutation, 2020, 41:5
   DOI: 10.1002/humu.23987
   PMCID: PMC7160051
7. An Integrated, Optofluidic System with Aligned Optical Waveguides, Microlenses, and Coupling Prisms for Fluorescence Sensing
   DS Park, BM Young, BH You, V Singh, SA Soper, MC Murphy
   IEEE Journal of Microelectromechanical Systems, 2020, 29(4):600-609.
   DOI: 10.1109/JMEMS.2020.3004374
   PMCID:
8. Robust, Transparent, Superhydrophobic Coatings Using Novel Hydrophobic/Hydrophilic Dual-sized Silica Particles
   X Zhao, DS Park, J Choi, S Park, SA Soper, MC Murphy
   Journal of Colloid and Interface Science, 2020, 574, 347-354.
   DOI: 10.1016/j.jcis.2020.04.065
   PMCID: PMC7256315
9. Application of multiplex bisulfite PCR-LDR-qPCR assay in interrogating bioinformatically-identified, blood-based methylation markers for colorectal cancer
   MD Bacolod, AH Mirza, J Huang, SF Giardina, PB Feinberg, SA Soper, F Barany
   Journal of Molecular Diagnostics, 2020, 22(7):885-900.
   DOI: 10.1016/j.jmoldx.2020.03.009
   PMCID: PMC7338890
10. Liquid Biopsy Markers for Stroke Diagnostics
    H Wijerathne, MA Witek, AE Baird, SA Soper
    Expert Review of Molecular Diagnostics, 2020, 20(8):771-788.
    DOI: 10.1080/14737159.2020.1777859
    PMCID:
11. Microfluidic gasketless interconnects sealed by superhydrophobic surfaces
    DS Park, X Zhao, SA Soper, MC Murphy
    JMEMS, 2020, 29(5):894-895
    DOI: 10.1109/JMEMS.2020.3000325
    PMCID: PMC7978084
12. Open‐Tubular Nanoelectrochromatography (OT‐NEC): Gel‐Free Separation of Single Stranded DNAs (ssDNAs) in Thermoplastic Nanochannels
    CA Amarasekara, US Athapattu, C Rathnayaka, J Choi, S Park, SA Soper
    Electrophoresis, 2020, 41(18-19):1627-1640.
    DOI: 10.1002/elps.202000109
    PMCID: PMC8107830
13. Affinity enrichment of extracellular vesicles from plasma reveals mRNA changes associated with acute ischemic stroke
    H Wijerathne, MA Witek, JM Jackson, V Brown, ML Hupert, K Herrera, C Kramer, AE Davidow, Y Li, AE Baird, MC Murphy, SA Soper
    Communications Biology, 3, 613 (2020)
    DOI: 10.1038/s42003-020-01336-y
    PMCID: PMC7589468

2019

1. Time-Delayed Integration--Spectral Flow Cytometer (TDI-SFC) for Low-Abundance-Cell Immunophenotyping
   W Hu, SA Soper, JM Jackson
   Analytical Chemistry, 2019, 91, 7, 4656-4664.
   DOI: 10.1021/acs.analchem.9b00021
   PMCID:PMC6554645
2. Chapter 7 – Single molecule analysis in nanofluidics devices
   KM Weerakoon-Ratnayake, S Vaidyanathan, CA Amarasekara, CK Johnson, SA Soper
   August 2019, 335-377.
   DOI: 10.1016/B978-0-12-816463-1.00007-9
3. Design and Fabrication of a Multi-scale fluidic Motherboard for a Universal Molecular Processing System (uMPS)
   DS Park, M Witek, X Zhao, Y Kang, K Dathathreya, SA Soper, MC Murphy
   Proceedings of the ASME IMECE 2019, Salt Lake City, UT, Nov 11-14, 2019. IMECE2019-11921
   DOI: 10.1115/IMECE2019-11921
4. Detection of CTCs from Whole Blood of Lung Cancer Patients Using the Automated Liquid Scan
   R Muller, S Purushotham, P Diaz, A Bartakova, J Muller-Cohn, J Lu, V Cheung, R Melnychuk, J Barber-Singh, E Fabio, H Husain, MA Witek, M Zomorrodi, ML Hupert, SA Soper, JM Jackson, C Chen
   Cancer Research, 79 (13 Supplement) 3984-3984. 2019
   DOI: 10.1158/1538-7445.AM2019-3984

2018

1. Accurate, Predictable, Repeatable Micro-Assembly Technology for Polymer, Microfluidic Modules
   TY Lee, K Han, D Barrett, S Park, SA Soper, M Murphy
   Sens. Actuators, B 254, 1249-1258 (2018).
   DOI: 10.1016/j.snb.2017.07.189
   PMCID: PMC5844477
2. Isolation of Circulating Plasma Cells from Blood of Patients Diagnosed with Clonal Plasma Cell Disorders using Cell Selection Microfluidics
   J Kamande, M Lindell, MA Witek, P Voorhees, SA Soper
   Integr. Biol. 10, 82-91, (2018).
   DOI: 10.1039/C7IB00183E
   PMCID: PMC5877822
3. Molecular Profiling of Liquid Biopsy Samples for Precision Medicine
   CDM Campos, JM Jackson, MA Witek, SA Soper
   The Cancer Journal 24, 93-103 (2018).
   DOI: 10.1097/PPO.0000000000000311
   PMCID: PMC5880307
4. Electrokinetic Transport Properties of Deoxynucleotide Monophosphates (dNMPs) through Thermoplastic Channels
   CE O’Neil, CA Amarasekara, KM Weerakoon-Ratnayake, B Gross, Z Jia, V Singh, S Park, SA Soper
   Analytica chimica acta 1027, 67-75 (2018).
   DOI: 10.1016/j.aca.2018.04.047
   PMCID: PMC6408931
5. Microfluidic-based Solid Phase Extraction of Cell Free DNA
   CDM Campos, S Thippalagamage, JM Jackson, MA Witek, DS Park, M Murphy, AK Godwin, SA Soper
   Lab Chip 18, 3459-3470 (2018).
   DOI: 10.1039/C8LC00716K
   PMCID: PMC6391159
6. Extracellular Vesicles (EVs) as Blood-Basesd Markers: Microfluidics for their Enrichment and Analysis
   SA Soper
   Abstracts of Papers of the American Chemical Society 2018, 255

2017

1. Discrete microfluidics for the isolation of circulating tumor cell subpopulations targeting fibroblast activation protein alpha and epithelial cell adhesion molecule
   MA Witek, RD Aufforth, H Wang, JW Kamande, JM Jackson, SR Pullagurla, ML Hupert, J Usary, WZ Wysham, D Hilliard, S Montgomery, V Bae-Jump, LA Carey, PA Gehrig, MI Milowsky, CM Perou, JT Soper, YE Whang, JJ Yeh, G Martin, SA Soper
   npj Precision Oncology 1 (1), 24
   DOI: 10.1038/s41698-017-0028-8
   PMCID: PMC5871807
2. Staphylococcus aureus extracellular vesicles (EVs): surface-binding antagonists of biofilm formation
   H Im, S Lee, SA Soper, RJ Mitchell
   Mol Biosyst. 2017 Nov 21;13(12):2704-2714
   DOI: 10.1039/c7mb00365j
   PMCID: PMC5873579
3. Materials and microfluidics: enabling the efficient isolation and analysis of circulating tumour cells
   JM Jackson, WA Witek, JW Kamande, SA Soper
   Chem Soc Rev. 2017 Jul 17;46(14):4245-4280
   DOI: 10.1039/c7cs00016b. Review.
   PMCID: PMC5576189
4. Thermoplastic nanofluidic devices for biomedical applications
   KM Weerakoon-Ratnayake, CE O'Neil, FI Uba, SA Soper
   Lab Chip. 2017 Jan 31;17(3):362-381
   DOI: 10.1039/c6lc01173j. Review.
   PMCID: PMC5285477
5. CD15+ granulocyte and CD8+ T lymphocyte based gene expression clusters for ischemic stroke detection
   MG Adamski, Y Li, E Wagner, C Seales-Bailey, N Bennett, H Yu, MC Murphy, SA Soper, AE Baird
   Medical Research Archives, [S.l.], v. 5, n. 11, Nov. 2017
   DOI: 10.18103/mra.v5i11.1597
6. Polymer-based Nanosensors using Flight-Time Identification of Mononucleotides for Single-Molecule Sequencing
   SA Soper, S Park, E Podlaha-Murphy
   Abstracts of Papers of the American Chemical Society 2017, 254

2016

1. Characterization of Activated Cyclic Olefin Copolymer: Effects of Ethylene/Norbornene Content on the Physiochemical Properties
   CE O’Neil, S Taylor, K Ratnayake, S Pullagurla, V Singh, SA Soper
   Analyst, 2016, 141, 6521-6532
   DOI: 10.1039/C6AN01448H
   PMCID: PMC5354357
2. Interrogating Surface Functional Group Heterogeneity of Activated Thermoplastics Using Super-Resolution Fluorescence Microscopy
   CE O’Neil, JM Jackson, SH Shim, SA Soper
   Anal. Chem., 2016, 88 (7), pp 3686-3696
   DOI: 10.1021/acs.analchem.5b04472
   PMCID: PMC5546217
3. Electrophoretic Separation of Single Particles Using Nanoscale Thermoplastic Columns
   KM Weerakoon-Ratnayake, FI Uba, NJ Oliver-Calixte, SA Soper
   Anal. Chem., 2016, 88 (7), pp 3569-3577
   DOI: 10.1021/acs.analchem.5b04065
   PMCID: PMC5555359
4. Microfluidics for the Detection of Minimal Residual Disease in Acute Myeloid Leukemia Patients using Circulating Leukemic Cells Selected from Blood
   JM Jackson, JB Taylor, MA Witek, SA Hunsucker, JP Waugh, Y Fedoriw, TC Shea, SA Soper, PM Armistead
   Analyst, 2016, 21;141 (2): 640-51
   DOI: 10.1039/c5an01836f
   PMCID: PMC4701594
5. Cancer: a Global Concern that Demands New Detection Technologies
   SA Soper, A Rasooly
   Analyst, 2016, 141, 367-370
   DOI: 10.1039/C5AN90101D
   PMCID: PMC4777894
6. Improved Clinical Sensitivity Detection of Circulating Tumor Cell Assays using a Dual Selection Strategy in Women with Epithelial Ovarian Cancer
   WZ Wysham, MA Witek, SA Soper, VL Bae-Jump
   Gynecologic Oncology, 2016, vol 141, Supplement 1, 138
   DOI: 10.1016/j.ygyno.2016.04.364
7. Book Chapter in “Circulating Tumor Cells: Isolation and Analysis” (John Wiley & Sons, Inc)
   Sinusoidal Microchannels with High Aspect Ratios for CTC Selection and Analysis
   JM Jackson, MA Witek, SA Soper
   April 2016, 85-119
   DOI: 10.1002/9781119244554.ch4
8. Digital Determination of Chemotherapeutic Drug-Induced Damage Sites in Single DNA Molecules using Nanofluidic Channels
   DG Kaufman, PD Chastain, SA Soper
   FASEB Journal 2016 30:1_supplement, 51.8-51.8
9. Nanosensors using Flight-Time Identification of Mononucleotides for Single-Molecule DNA Sequencing
   SA Soper
   Abstracts of Papers of the American Chemical Society 2016, 252

2015

1. Investigation of Surface Charge and Electroosmotic Flow in Polymer Nanoslits and Nanochannels
   FI Uba, SR Pullagurla, N Sirasunthorn, J Wu, S Park, R Chantiwas, Y Cho, H Shin, SA Soper
   Analyst 140 (2015) 113-126.
   DOI: 10.1039/C4AN01439A
   PMCID: PMC4280799
2. High Process Yield Rates of Thermoplastic Nanofluidic Devices using a Hybrid Thermal Assembly Technique
   FI Uba, B Hu, K Weerakoon-Ratnayake, N Oliver-Calixte, SA Soper
   LOC 15 (2015) 1038-1049. This appeared on the cover of the journal and has been a feature article in their blog.
   DOI: 10.1039/C4LC01254B
   PMCID: PMC4315742
3. Enzymatic Cleavage of Uracil-Containing Single-Stranded DNA Linkers for the Efficient Release of Affinity-Selected Circulating Tumor Cells
   S Nair, JM Jackson, MA Witek, V Bae-Jump, PA Gehrig, WZ Wysham, PM Armistead, P Voorhees, SA Soper
   Chemical Communications 51 (2015) 3266-3269.
   DOI:  10.1039/C4CC09765C
   PMCID: PMC4552044
4. Current and Future Bioanalytical Approaches to Stroke Assessment
   S Pullagurla, A Baird, SA Soper
   Bioanalysis 7 (2015) 1017-1035.
   DOI: 10.4155/bio.15.40
5. Recent and Near-Future Advances in Nucleic Acid-based Diagnosis of Stroke
   AE Baird, SA Soper, S Pullagurla, M Adamski
   Expert Review of Molecular Diagnostics 5 (2015) 665-679.
   DOI: 10.1586/14737159.2015.1024660
6. Rapid Assessment of Minimal Residual Acute Myeloid Leukemia from Peripheral Blood Using a Microfluidic Chip
   JM Jackson, J Taylor, MA Witek, SA Hunsucker, JP Waugh, YD Fedoriw, TC Shea, SA Soper, PM Armistead
   Blood 126 (2015) 1389.
   DOI: 10.1182/blood.V126.23.1389.1389
7. Electrophoretic Transport of Single DNA Nucleotides through Nanoslits: A Molecular Dynamics Simulation Study
   K Xia, BR Novak, KM Weerakoon-Ratnayake, SA Soper, DE Nikitopoulos, D Moldovan
   J. Phys. Chem. B, 2015, 119 (35), pp 11443-11458.
   DOI: 10.1021/acs.jpcb.5b02798