108. Byrd C., Alkhamis O., Castro G., Nguyen T. & Xiao Y. (2026) High-throughput aptamer characterization via real-time nuclease digestion. J. Am. Chem. Soc.148, 10421 – 10436

107. Alkhamis O., Canoura J., Castro G., Byrd C., Bryant A., Yu H.X. & Xiao Y. (2026) Affinity maturation of a fentanyl aptamer by motif-SELEX. JACS Au, 6, 434 – 445

106.   Bacon A., Alkhamis O., Byrd C., Perry J., Canoura J. & Xiao Y. (2025) Reagentless real-time ATP monitoring with new DNA aptamers. Small e08898

105.   Nguyen T., Alkhamis O., Bacon A., Bukhryakov K.V., Vinueza N.R. & Xiao Y. (2025) High-contrast aptamer-based merocyanine displacement assay for sensitive small molecule detection. ACS sensors 10, 7799 – 7809

104.   Alkhamis O., Byrd C., Canoura J., Bacon A., Hill R. & Xiao Y. (2025) Exploring the relationship between aptamer binding thermodynamics, affinity, and specificity. Nucleic Acids Res. 53, gkaf219

103.   Yu H. X., Canoura J., Byrd C., Alkhamis O., Bacon A., Yan A., Sullenger B.A. & Xiao Y. (2025) Improving aptamer affinity and determining sequence-activity relationships via motif-SELEX. J. Am. Chem. Soc. 147, 9472 – 9486

102.   Wang L.L., Canoura J., Byrd C., Nguyan T., Alkhamis O., Ly P. & Xiao Y. (2024) Examining the relationship between aptamer complexity and molecular discrimination of a low-epitope target. ACS Cent. Sci. 10, 2213 – 2228

101.   Canoura J., Alkhamis O., Byrd C., Wang L.L., Bryant A. & Xiao Y. (2024) Determining the precision of high throughput sequencing and its influence on aptamer selection. Anal. Chem. 96, 17720 – 17729

100.   Wang L.L., Alkhamis O., Canoura J., Yu H.X. & Xiao Y. (2024) Rapid nuclease-assisted selection of high-affinity small-molecule aptamers. J. Am. Chem. Soc. 146, 21296 – 21307

99.     Canoura J., Nguyen T., Byrd C., Hill R., Liu Y.Z. & Xiao Y. (2024) Generation of high-affinity aptamers for indozole synthetic cannabinoids. Anal. Chem. 96, 11488 – 11497

98.     Alkhamis O., Canoura J., Wang L.L. & Xiao Y. (2024) Nuclease-assisted selection of slow-off rate aptamers. Sci. Adv. 10, eadl3426

97.     Canoura J., Alkhamis O., Venzke M., Ly P.T. & Xiao Y. (2024) Developing aptamer-based colorimetric opioid tests. JACS Au 4, 1059 – 1072

96.     Yang K. Alkhamis O., Canoura J. Bryant A., Gong E.M., Barbu M., Taylor S., Nikic D., Banerjee S., Xiao Y., Stojanovic M.N. & Landry D.W. (2024) Exploring the landscape of aptamers: From cross-reactive, to selective, to specific, high-affinity receptors for cocaine. JACS Au 4, 760 – 770

95.     Alkhamis O., Canoura J., Wu Y., Emmons N.A., Wang Y., Honeywell K.M., Plaxco K.W. Kippin T.E. & Xiao Y. (2024) High-affinity aptamers for in vitro and in vivo cocaine sensing. J. Am. Chem. Soc. 146, 3230 – 3240

94.     Canoura J., Liu Y.Z., Alkhamis O. & Xiao Y. (2023) Aptamer-based fentanyl detection in biological fluids. Anal. Chem. 95, 18258 – 18267

93.     Alkhamis O., Canoura J., Ly P.T. & Xiao Y. (2023) Using exonuclease for aptamer characterization, engineering, and sensing. Acc. Chem. Res. 56, 1731 – 1743

92.     Alkhamis O., Canoura J., Willis C., Wang L.L., Perry J. & Xiao Y. (2023) Comparison of aptamer signaling mechanisms reveals disparities in sensor response and strategies to eliminate false signals. J. Am. Chem. Soc. 145, 12407 – 12422

91.     Canoura J., Liu Y.Z., Perry J., Willis C. & Xiao Y. (2023) Suite of aptamer-based sensors for the detection of fentanyl and its analogs. ACS sensors 8, 1901 – 1911

90.     Alkhamis O. & Xiao Y. (2023) Systematic study of in vitro selection stringency reveals how to enrich high-affinity aptamers. J. Am. Chem. Soc. 145, 194 – 206

89.     Canoura J., Liu Y.Z., Alkhamis O., Willis C. & Xiao Y. (2023) High-throughput quantitative binding analysis of DNA aptamers using exonucleases. Nucleic Acids Res. 51, e19

88.     Jin X., Liu Y.Z., Alkhamis O., Canoura J., Bacon A., Xu R.Y., Fu, F.F. & Xiao Y. (2022) Near-infrared dye-aptamer assay for small molecule detection in complex specimens. Anal. Chem. 94, 10082 – 10090

87.     Alkhamis O., Canoura J., Bukhryakov K.V., Tarifa A., DeCaprio A.P. & Xiao Y. (2022) DNA aptamer-cyanine complexes as generic colorimetric small-molecule sensors. Angew. Chem. Int. Ed., 61, e202112305

86.     Paudyal J., Wang P., Zhou F., Liu Y.Z., Cai Y. & Xiao Y. (2021) Platinum-nanoparticle-modified single-walled carbon nanotube-laden paper electrodes for electrocatalytic oxidation of methanol. ACS Appl. Nano Mater. 4, 13798 – 13806

85.     Liu Y.Z., Liu X.T., Alkhamis O., Yu H.X., Canoura J. & Xiao Y. (2021) Aptamer-integrated paper electrochemical device for multi-analyte detection. ACS Appl. Mater. Interfaces. 13, 17330 – 17339

84.     Liu Y.Z., Canoura J, Alkhamis O. & Xiao Y. (2021) Immobilization strategies for enhancing sensitivity of electrochemical aptamer-based sensors. ACS Appl. Mater. Interfaces. 13, 9491 – 9499

83.     Yu H.X., Luo Y.P., Alkhamis O., Canoura J., Yu B.Y. & Xiao Y.(2021) Isolation of natural DNA aptamers for challenging small-molecule targets – cannabinoids. Anal. Chem. 93, 3172 – 3180

82.     Yu H.X., Alkhamis O., Canoura J. and Liu Y.Z. & Xiao Y. (2021) Advances and challenges in small-molecule aptamer isolation, characterization and sensing. Angew. Chem. Int. Ed., 133, 2 – 26

81.     Yu H. X., Chen Z.M., Liu Y.Z., Alkhamis O., Song Z.P. & Xiao Y. (2021) Fabrication of aptamer-modified paper electrochemical devices for on-site biosensing. Angew. Chem. Int. Ed. 60, 2993 – 3000

80.     Canoura J., Yu H.X., Alkhamis O., Roncancio R., Farhana R. and Xiao Y. (2021) Accelerating post-SELEX aptamer engineering using exonuclease digestion. J. Am. Chem. Soc., 143, 805 – 816

79.     Alkhamis O., Yang W.J., Farhana R., Yu H.X. and Xiao Y. (2020) Label-free profiling of DNA aptamer-small molecule binding using T5 exonuclease. Nucleic Acids Res., 48(20), e120

78.     Liu Y.Z., Yu H.X., Alkhamis O., Moliver J. & Xiao Y. (2020) Tuning biosensor cross-reactivity using aptamer mixtures. Anal. Chem. 92, 5041 – 5047 

77.     Wu Y., Belmonte I., Sykes, K., Xiao, Y. & White R. (2019) A perspective on the future role of aptamers in analytical chemistry. Anal. Chem. 91, 15335 – 15344 

76.     Alkhamis O., Canoura J., Yu H.X., Liu Y.Z. & Xiao Y. (2019) Innovative engineering and sensing strategies for aptamer-based small-molecule detection. Trends Anal. Chem. 121, 115699

75.     Gao H.L., Zhao, J.X., Huang Y., Cheng X., Wang S., Han Y., Xiao Y. & Lou X.H. (2019) Universal design of structure-switching aptamers with signal reporting functionality. Anal. Chem. 91, 14514 – 14521

74.     Yang W.J., Yu H.X., Alkhamis O., Liu Y.Z., Canoura, J., Fu F.F. & Xiao Y. (2019) In vitro isolation of class-specific oligonucleotide-based small-molecule receptors. Nucleic Acids Res., 47(12), e71

73.     Luo Y.P., Yu H.X., Alkhamis O., Liu Y.Z., Lou X.H., Yu B.Y. & Xiao Y. (2019) Label-free, visual detection of small molecules using highly target-responsive multi-module split aptamer constructs. Anal. Chem. 91, 7199 – 7207

72.     Canoura J., Wang Z.W., Yu H.X., Alkhamis O., Fu F.F. & Xiao Y. (2018) No Structure-switching required: A generalizable exonuclease-mediated aptamer-based assay for small-molecule detection. J. Am. Chem. Soc., 140, 9961 – 9971

71.     Wang Z.W., Yu H.X., Canoura J., Liu Y.Z., Alkhamis O., Fu F.F. & Xiao Y. (2018) Introducing structure-switching functionality into small-molecule-binding aptamers via nuclease-directed truncation. Nucleic Acids Res., 46(13), e81

70.     Yu H.X., Yang W.J., Alkhamis O., Canoura J., Yang K. & Xiao Y. (2018) In vitro isolation of small-molecule-binding aptamers with intrinsic dye-displacement functionality. Nucleic Acids Res., 46(8), e43

69.     Yu H.X., Canoura J., Guntupalli B., Alkhamis O. & Xiao Y. (2018) Sensitive detection of small-molecule targets using cooperative binding split aptamers and enzyme-assisted target recycling. Anal. Chem. 90, 1748 – 1758

68.     Liang P.P., Canoura J., Yu H.X., Alkhamis O. & Xiao Y. (2018) Dithiothreitol-regulated coverage of oligonucleotide-modified gold nanoparticles to achieve optimized biosensor performance. ACS Appl. Mater. Interfaces. 10, 4233 – 4242

67.     Yu H.X., Xu X.W., Liang P.P., Loh K.Y., Guntupalli B., Roncancio D. & Xiao Y. (2017) A broadly-applicable assay for rapidly and accurately quantifying DNA surface coverage on diverse particles. Bioconjugate Chem., 28, 933 – 943

66.     Yu H.X., Canoura J., Guntupalli B., Lou X.H. & Xiao Y. (2017) A cooperative-binding split aptamer assay for rapid, specific and ultra-sensitive fluorescence detection of cocaine in saliva. Chem. Sci., 8, 131 – 141

65.     Xu Q., Lou X.H., Wang L., Ding X.F., Yu H.X. & Xiao Y. (2016) Rapid, surfactant-free, and quantitative functionalization of gold nanoparticles with thiolated DNA under physiological pH and its application in molecular beacon-based biosensor. ACS Appl. Mater. Interfaces. 8, 27298 – 27304

64.     Guntupalli B., Liang P.P., Lee J.H., Yang Y.H., Yu H.X., Canoura J., He J., Li W.Z., Weizmann Y. & Xiao Y. (2015) Ambient filtration method to rapidly prepare highly conductive, paper-based porous gold films for electrochemical biosensing. ACS Appl. Mater. Interfaces, 7, 27049 – 27058

63.     Zhao T., Liu R., Ding X.F., Zhao J.C., Yu H.X., Wang L., Xu Q., Wang X., Lou X.H., He M. & Xiao Y. (2015) Nanoprobe-enhanced, split aptamer-based electrochemical sandwich assay for ultrasensitive detection of small molecules. Anal. Chem., 87, 7712 – 7719

62.     Liang P.P., Yu H.X., Guntupalli B. & Xiao Y. (2015) Paper-based device for rapid visualization of NADH based on dissolution of gold nanoparticles. ACS Appl. Mater. Interfaces, 7, 15023 – 15030

61.     Roncancio D., Yu H.X., Xu X.W., Wu S., Liu R., Debord J., Lou X.H. & Xiao Y. (2014) A label-free aptamer-fluorophore assembly for rapid and specific detection of cocaine in biofluids. Anal. Chem., 86, 11100 – 11106

60.     Wu S., Liang P.P., Yu H.X., Xu X.W., Liu Y., Lou X.H. & Xiao Y. (2014) Amplified single base-pair mismatch detection via aggregation of exonuclease-sheared gold nanoparticles. Anal. Chem., 86, 3461 – 3467

59.     Oh S.S., Plakos K., Xiao Y., Eisenstein M. & Soh H.T. (2013) In vitro selection of shape-changing DNA nanostructures capable of binding-induced cargo release. ACS Nano, 7, 9675 – 9683

58.     Lou X.H., Zhao T., Liu R., Ma J. & Xiao Y. (2013) Self-assembled DNA monolayer buffered dynamic ranges of mercuric electrochemical sensor. Anal. Chem., 85, 7574 – 7580

57.     Deborggraeve S., Dai J.Y., Xiao Y. & Soh H.T. (2013) Controlling the function of DNA nanostructures with specific trigger sequences. Chem. Commun., 49, 397 – 399

56.     Ahmad K.M., Xiao Y. & Soh H.T. (2012) Selection is more intelligent than design: improving the affinity of a bivalent ligand through directed evolution. Nucleic Acids Res., 40, 11777 – 11783

55.     Feng L.Y., Zhao C.Q., Xiao Y., Wu L., Ren J.S. & Qu X.G. (2012) Electrochemical DNA three-way junction-based sensor for distinguishing chiral metallo-supramolecular complexes. Chem. Commun., 48, 6900 – 6902

54.     Zuo X.L., Xia F., Patterson A., Soh H.T. Xiao Y. & Plaxco K.W. (2011) Two-step, PCR-free telomerase detection by using exonuclease III-aided target recycling. ChemBioChem, 12, 2745 – 2747

53.     Olmsted I.R., Xiao Y., Cho M., Csordas A.T., Sheehan J.H, Meiler J., Soh H.T. & Bornhop D.J. (2011) Measurement of aptamer-protein interactions with back-scattering interferometry. Anal. Chem., 83, 8867 – 8870

52.     Hsieh K.W., White R.J., Ferguson B.S., Plaxco K.W., Xiao Y. & Soh H.T. (2011) Polarity-switching electrochemical sensor for specific detection of single-nucleotide mismatches. Angew. Chem., Int. Ed., 50, 11176 – 11180

51.     Ahmad K.M., Oh S.S., Kim S., McClellen F.M., Xiao Y. & Soh H.T. (2011) Probing the limits of aptamer affinity with a microfluidic SELEX platform. PLoS ONE, 6, e27051

50.     Oh S.S., Ahmad K.M., Cho M., Kim S., Xiao Y. & Soh H.T. (2011) Improving aptamer selection efficiency through volume dilution, magnetic concentration, and continuous washing in microfluidic channels. Anal. Chem., 83, 6883 – 6889

49.     Ferguson B.S., Buchsbaum S.F., Wu T.T., Hsieh K.W., Xiao Y., Sun R. & Soh H.T. (2011) Genetic analysis of H1N1 influenza virus from throat swab samples in a microfluidic system for point-of-care diagnostics. J. Am. Chem. Soc., 133, 9129 – 9135

48.     Wang J.P., Liu Y.L., Teesalu T., Sugahara K.N., Kotamrajua V.R., Adams J.D., Ferguson B.S., Gong Q., Oh S.S., Csordas A.T., Cho M., Ruoslahti E., Xiao Y. & Soh H.T. (2011) Selection of phage-displayed peptides on live adherent cells in microfluidic channels. Proc. Natl. Acad. Sci. U.S.A., 108, 6909 – 6914

47.     Xiao Y., Dane K.Y., Uzawa T., Csordas A., Qian J.R., Soh H.T., Daugherty P.S., Lagally E.T., Heeger A.J. & Plaxco K.W. (2010) Detection of telomerase activity in high concentration of cell lysates using primer-modified gold nanoparticles. J. Am. Chem. Soc., 132, 15299 – 15307

46.     Xia F., White R.J., Zuo X.L., Patterson A., Xiao Y., Kang D., Gong X., Plaxco K.W. & Heeger A.J. (2010) An electrochemical super-sandwich assay for sensitive and selective DNA detection in serum. J. Am. Chem. Soc., 132, 14346 – 14348

45.     Cho M., Xiao Y., Nie J., Stewart R., Csordas A.T., Oh S.S., Thomson J.A. & Soh H.T. (2010) Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing. Proc. Natl. Acad. Sci. U.S.A., 107, 15373 – 15378

44.     Oh S.S., Plakos K.J.I., Lou X.H., Xiao Y. & Soh H.T. (2010) In vitro selection of structure-switching, self-reporting aptamers. Proc. Natl. Acad. Sci. U.S.A., 107, 14053 – 14058

43.     Xia F., Zuo X.L., Yang R.Q., White R.J., Xiao Y., Kang D., Gong X., Lubin A.A., Vallée-Bélisle A., Yuen J.D., Hsu B.Y.B. & Plaxco K.W. (2010) Label-free, dual-analyte electrochemical biosensors: a new class of molecular-electronic logic gates. J. Am. Chem. Soc., 132, 8557 – 8559

42.     Xia F., Zuo X.L., Yang R.Q., Xiao Y., Kang D., Vallée-Bélisle A., Gong X., Yuen J.D., Hsu B.Y.B., Heeger A.J. & Plaxco K.W. (2010) Colorimetric detection of DNA, small molecules, proteins and ions, using unmodified gold nanoparticles and conjugated polyelectrolytes. Proc. Natl. Acad. Sci. U.S.A., 107, 10837 – 10841

41.     Hsieh K.W., Xiao Y. & Soh H.T. (2010) Electrochemical DNA detection via exonuclease and target-catalyzed transformation of surface-bound probes. Langmuir, 26, 10392 – 10396

40.     Zuo X.L., Xia F., Xiao Y. & Plaxco K.W. (2010) Sensitive and selective, amplified fluorescence DNA detection based on Exonuclease III-aided target recycling. J. Am. Chem. Soc., 132, 1816 – 1818

39.     Xia F., Zuo X.L., Yang R.Q., Xiao Y., Kang D., Vallée-Bélisle A., Gong X., Heeger A.J. & Plaxco K.W. (2010) On the binding of cationic, water-soluble conjugated polymer to DNA: electrostatic and hydrophobic interactions. J. Am. Chem. Soc., 132, 1252 – 1254

38.     Csordas A.T., Gerdon A.E., Adams J.D., Qian J.R., Oh S.S., Xiao Y. & Soh H.T. (2010) Detection of proteins in serum via micromagnetic aptamer PCR (MAP) technology. Angew. Chem., Int. Ed., 49, 355 – 358

37.     Xiao Y., Lou X.H., Uzawa T., Plakos K.J.I., Plaxco K.W. & Soh H.T. (2009) An electrochemical sensor for single nucleotide polymorphism detection in serum based on a triple-stem DNA probe. J. Am. Chem. Soc., 131, 15311 – 15316

36.     Peng Y.H., Wang X.H., Xiao Y., Feng L.Y., Zhao C., Ren J.S. & Qu X.G. (2009) I-Motif quadruplex DNA-based biosensor for distinguishing single- and multiwalled carbon nanotubes. J. Am. Chem. Soc., 131, 13813 – 13818

35.     Lou X.H., Xiao Y., Wang Y., Mao H.G. & Zhao J.L. (2009) Label-free colorimetric screening of nuclease activity and substrates by using unmodified gold nanoparticles. ChemBioChem, 10, 1973 – 1977

34.     Oh S.S., Qian J.R., Lou X.H., Zhang Y.T., Xiao Y. & Soh H.T. (2009) Generation of highly specific aptamers via micromagnetic selection. Anal. Chem., 81, 5490 – 5495

33.     Xiao Y., Uzawa T., White R.J., DeMartini D. & Plaxco K.W. (2009) On the signaling of electrochemical aptamer-based sensors: collision- and folding-based mechanisms.  Electroanalysis, 21, 1267 – 1271

32.     Zuo X.L., Xiao Y. & Plaxco K.W. (2009) High specificity, electrochemical sandwich assays based on single aptamer sequences and suitable for the direct detection of small-molecule targets in blood and other complex matrices. J. Am. Chem. Soc., 131, 6944 – 6945    

31.     Swensen J.S., Xiao Y., Ferguson B.S., Lubin A.A., Lai R.Y., Heeger A.J., Plaxco K.W. & Soh H.T. (2009) Continuous, real-time monitoring of cocaine in undiluted blood serum via a microfluidic electrochemical aptamer-based sensor. J. Am. Chem. Soc., 131, 4262 – 4266

30.     Lou X.H., Qian J.R., Xiao Y., Viel L., Gerdon A.E., Lagally E.T., Atzberger P., Tarasow T.M., Heeger A.J. & Soh H.T. (2009) Micromagnetic selection of aptamers in microfluidic channels. Proc. Natl. Acad. Sci. U.S.A., 106, 2989 – 2994

29.     Cash K.J., Heeger A.J., Plaxco K.W. & Xiao Y. (2009) Optimization of a reusable, DNA pseudoknot-based electrochemical sensor for sequence-specific DNA detection in blood serum. Anal. Chem., 81, 656 – 661

28.     Xiao Y., Plakos K.J.I., Lou X.H., White R.J., Plaxco K.W. & Soh H.T. (2009) Fluorescence detection of single-nucleotide polymorphisms with a single, self-complementary, triple-stem DNA probe. Angew. Chem., Int. Ed., 48, 4354 – 4358

27.     White R.J., Phares N., Lubin A.A., Xiao Y. & Plaxco K.W. (2008) Optimization of electrochemical aptamer-based sensors via optimization of probe packing density and surface chemistry. Langmuir, 24, 10513 – 10518

26.     Xiao Y., Qu X.G., Plaxco K.W. & Heeger A.J. (2007) Label-free electrochemical detection of DNA in blood serum via target-induced resolution of an electrode-bound DNA pseudoknot. J. Am. Chem. Soc., 129, 11896 – 11897

25.     Xiao Y., Rowe A.A. & Plaxco K.W. (2007) Electrochemical detection of parts-per-billion lead via an electrode-bound DNAzyme assembly. J. Am. Chem. Soc., 129, 262 – 263

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Patents

21.    Alkhamis O. & Xiao Y. “Method for identifying multiparatopic aptamers for cardiac troponin and usage of aptamers for detection.” 2026, patent provision

20. Wang L. & Xiao Y. “Color test for fentanyl analogs.” 2026, patent provision

19.    Wang L. & Xiao Y. “Methods and compositions of aptamers for detection of low complexity molecules.” 2026, patent provision

18.    Liu Y.Z., Canoura J. & Xiao Y. “Immobilization strategies for enhancing sensitivity of electrochemical aptamer-based sensors.” 2025, US12,455,256

17. Canoura J. & Xiao Y. “Compositions and methods related to aptamer-based colorimetric assays.” 2025, US20250115919A1

16. Liu Y.Z., Canoura J. & Xiao Y. “Immobilization strategies for enhancing sensitivity of electrochemical aptamer-based sensors.” 2023, US11796499B2; 2025, US12455256B2

15. Alkhamis O. & Xiao Y. “Nuclease-assisted selection of slow-off rate aptamers.” 2023, patent provision

14.    Xiao Y., Alkhamis O. & Yu H.X. “DNA aptamer-cyanine complexes as mephedrone and cannabinoid colorimetric sensors.” 2023, US011656235B2

13.     Canoura J. & Xiao Y. “Aptamer-based sensors for detection of fentanyl opioids.” 2023, US Patent 11579110; 2022, US Patent 11408850

12.     Xiao Y. & Yu H.X. “Aptamers that bind to natural and synthetic cannabinoids.” 2021, US Patent 10907163

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