Journal Articles

174.  Liu M, Yin Q, Brennan JD, Li Y. (2017). Selection and Characterization of DNA Aptamers for Detection of Glutamate Dehydrogenase from Clostridium difficile. Biochimie. pii: S0300-9084(17)30224-9. doi: 10.1016/j.biochi.2017.08.015.

173.  Ali MM, Brown CL, Jahanshahi-Anbuhi S, Kannan B, Li Y, Filipe CDM, Brennan JD. (2017). A Printed Multicomponent Paper Sensor for Bacterial Detection. Sci. Rep. 7, 12335.

172.  Liu M, Chang D, Li Y. (2017). Discovery and Biosensing Applications of Diverse RNA-Cleaving DNAzymes. Acc. Chem. Res. 50, 2273-2283.

171. Carrasquilla C, Kapteyn E, Li Y and Brennan JD (2017). Sol-Gel Derived Biohybrid Materials Incorporating Long-Chain DNA Aptamers. Angew. Chem. Int. Ed. 56, 10686-10690.

170. Chang D, Tram K, Li B, Feng Qian, Shen Z, Lee CH, Salena BJ, and Li Y (2017). Detection of DNA Amplicons of Polymerase Chain Reaction Using Litmus Test. Sci. Rep. 7, 3110.

169. Manochehry S, Liu M, Chang D, Li Y (2017). Optical Biosensors Utilizing Graphene and Functional DNA Molecules. J. Mater. Res. 32, 2973-2983.

168. Liu M, Zhang Q, Chang D, Gu J, Brennan JD, and Li Y (2017). A DNAzyme Feedback Amplification Strategy for Biosensing. Angew. Chem. Int. Ed. 2017 56, 6142-6146.

167. Zhang A, Chang D, Zhang Z, Li F, Li W, Wang X, Li Y and Hua Q. (2017). In vitro selection of DNA aptamers that binds geniposide. Molecules. 22, 383.

166. Jahanshahi-Anbuhi S, Kannan B, Pennings, K, Leung V, Giang K, Wang J, Li Y, Pelton R, Brennan JD, Filipe CD (2017). Automating Multi-Step Paper-Based Assays Using Integrated Layering of Reagents. Lab Chip. 17, 943-950.

165. Islam MS, Kuryllo K, Shahid A, Li Y, M. Deen MJ, Selvaganapathy PR (2017). Electrophoretic concentration and electrical lysis of bacteria in a microfluidic device using a nanoporous membrane. Micromachines. 8, 45.

164. Hsieh P-Y, Ali MM, Tram K, Jahanshahi-Anbuhi S, Brown CL, Brennan JD, Filipe CD, Li Y (2017). RNA Protection is Effectively Achieved by Pullulan Film Formation. ChemBioChem. 18, 502-505.

163. Chang D, Zakaria S, Deng M, Allen N, Tram K, Li Y (2016). Integrating Deoxyribozymes into Colorimetric Sensing Platforms. Sensors. 16, 2061.

162. Liu M, Zhang Q, Li Z, Gu J, Brennan JD, Li Y (2016). Programming a Topologically Constrained DNA Nanostructure into a Sensor. Submitted to Nat. Commun. 7, 12074.

161. Tram K, Manochehry S, Feng Q, Chang D, Salena BJ, Li Y (2016). Colourimetric Detection of Bacteria Using Litmus Test. J. Vis. Exp. (115), e54546, doi:10.3791/54546.

160. Zhang W, Feng Q, Chang D, Tram K, Li Y (2016). In Vitro Selection of RNA-cleaving DNAzymes for Bacterial Detection. Methods. 106, 66-75.

159. Wu Z, Tram K, Salena BJ, Li Y (2016). Topological DNA Assemblies Containing Identical or Fraternal Twins. ChemBioChem. 17, 1142-5.

158. Jahanshahi-Anbuhi S, Kannan B, Leung V, Liu M, Carrasquila C, White D, Li Y, Pelton R, Brennan JD, Filipe CD (2016). Simple and Ultrastable All-in-One Tablets for Challenging Bioassays. Chem Sci. In press.

157. Lee CH, Steiner T, Petrof E, Smieja M, Roscoe D, Nematallah A, Weese J, Collins S, Moayyedi P, Crowther M, Ropeleski M, Padman J, Higgins D, Li Y, Rau N, Kim P (2016). A randomized trial of fresh vs. frozen fecal transplantation for C. difficile Infection. The Journal of the American Medical Association (JAMA). In press.

156. Liu M, Hui CY, Zhang Q, Gu J, Kannan B, Jahanshahi-Anbuhi S, Filipe CD, Brennan JD, Li Y (2016). Target-induced and Equipment-free DNA Amplification with a Simple Paper Device. Angew. Chem. Int. Ed. Very Important Paper. In press. Featured as front cover.

155. Shen Z, Wu Z, Chang D, Zhang W, Tram K, Lee C, Kim P, Salena BJ, Li Y (2016). A Catalytic DNA Activated by a Specific Strain of Bacterial Pathogen. Angew. Chem. Int. Ed. Hot Paper. In press.

154. Liu M, Zhang W, Chang D, Zhang Q, Brennan J D, Li Y. (2016). Integrating graphene oxide, functional DNA and nucleic acid-manipulating strategies for amplified biosensing. Trends Anal. Chem. 74, 120-129.

153. Li Y (2015). A Quarter Century of In Vitro Selection. J Mol Evol. 81, 137-139.

152. Chan L, Tram K, Gysbers R, Gu J, Li Y (2015). Sequence Mutation and Structural Alteration Transform a Noncatalytic DNA Sequence into an Efficient RNA-Cleaving DNAzyme. J Mol Evol. 81, 245-253.

151. Kannan B, Jahanshahi-Anbuhi S, Pelton RH, Li Y, Filipe CD, Brennan JD (2015). Printed Paper Sensors for Serum Lactate Dehydrogenase using Pullulan-Based Inks to Immobilize Reagents. Anal. Chem. 87(18):9288-93.

150. Liu M, Zhang W, Zhang Q, Brennan JD, Li Y (2015). Biosensing via Tandem Reactions of Structure Switching, Nucleolytic Digestion and DNA Amplification of a DNA Assembly. Angew. Chem. Int. Ed. 54(33), 9637-41.

149. Gysbers R, Tram K, Gu J, Li Y (2015). Evolution of an Enzyme from a Noncatalytic Nucleic Acid Sequence. Scientific Reports. 5: 11405.

148. Tram K, Xia J, Gysbers R, Li Y. (2015). An efficient catalytic DNA that cleaves L-RNA. Submitted to PLoS One. 10(5):e0127751.

147. Mao Y, Liu M, Tram K, Gu J, Salena BJ, Jiang Y, Li Y (2015). Optimal DNA Templates for Rolling Circle Amplification Revealed by In Vitro Selection. Chem. Euro J. 21(22):8069-74.

146. Carrasquilla C, Little J, Li Y,  Brennan JD (2015). Patterned Paper Sensors Printed with Concatemeric DNA Aptamers. Chem. Euro J. 21(20):7369-73.

145. Chen T, Tian X, Liu C, Ge J, Chu X, Li Y (2015). Fluorescence Activation Imaging of Cytochrome c Released from Mitochondria Using Aptameric Nanosensor. J. Am. Chem. Soc. 137, 982-989.

144. He S, Qu L, Shen Z, Tan Y, Zeng M, Liu F, Jiang Y, Li Y (2015). Highly specific recognition of breast tumors by an RNA-cleaving fluorogenic DNAzyme probe. Anal Chem. 87, 569-577.

143. Qu, L., Ali, M. M., Aguirre, S. D., Liu, H., Jiang, Y., Li, Y. (2014). Examination of Bacterial Inhibition Using a Catalytic DNA. PLoS ONE. 9: e115640. Recommended by Faculty 1000 Prime.

142. Kuryllo, K, Jahanshahi, S., Zhu, W., Brown, E. D & Li, Y. (2014). A Dual Reporter System for Detecting RNA Interactions in Bacterial Cells. ChemBioChem. 15, 2703-9. Featured as the Inside Cover.

141. Tram, K., Kanda, P., Salena, B. J., Huan, S., Li, Y. (2014). Translating bacterial detection into a litmus test. Angew. Chem. Int. Ed. 53, 12799-802. doi: 10.1002/anie.201407021. Very Important Paper (top 5% papers). Featured as the Back Cover.

140. Zhang, Z., Wang, J., Ng, R., Li, Y., Wu, Z., Leung, V., Imbrogno, S., Pelton, R., Brennan, J. D., and Filipe, C. D. M. (2014) An Inkjet-Printed Bioactive Paper Sensor that Reports ATP through Odour Generation. Analyst. 139, 4775-4778.

139. Song, J., Lau, P. S., Liu, M., Shuang, S., Dong, C., Li, Y. (2014). A General Strategy to Create RNA Aptamer Sensors Using “Regulated” Graphene Oxide Adsorption. ACS Appl. Mater. Interfaces. DOI: 10.1021/am502138n. 

138. Wu, Z, Shen, Z., Tram, K., Li, Y.* (2014). Engineering interlocked DNA rings with minimal physical interactions. Nat. Commun. 5:4279.

137. Liu, M., Song, J., Shuang, S., Dong, C., Brennan, J. D., Li, Y.* (2014). A Graphene-Based Biosensing Platform Based on the Release of DNA Probes and Rolling Circle Amplification. ACS Nano. 8(6):5564-73.

136. Jahanshahi-Anbuhi, S., Pennings, K., Leung, V., Liu, M., Carrasquilla, C., Kannan, B., Li, Y., Pelton, R., Brennan, J. D.,* Filipe, C. D.* (2014). Pullulan Encapsulation of Labile Biomolecules to Give Stable Bioassay Tablets. Angew. Chem. Int. Ed. 53, 6155-6158.

135. Hui, C., Li, Y. Brennan, J. D. (2014). Fluorescence Analysis of the Properties of Structure-Switching DNA Aptamers Entrapped in Sol-Gel-Derived Silica Materials. Chem. Mater. 26, 1896-1904.

134. Mok, W. W. K., Li, Y. (2014). Therapeutic Peptides: New arsenal against drug resistant pathogens. Curr Pharm Des. 20, 771-92.

133. Wang, L., Tram, K., Ali, M. M., Salena, B., Li, J., Li, Y. (2014) Arrest of Rolling Circle Amplification by DNA Aptamers. Chemistry 20, 2420-4. doi: 10.1002/chem.201304292.

132. Bian, W., Ma, J., Liu, Q., Wei, Y., Li, Y., Dong, C., Shuang, S. (2014). A novel phosphorescence sensor for Co2+ ion based on Mn-doped ZnS quantum dots. Luminescence. 29(2):151-7.

131. Xu, Y., Ali, M. M., Sauder, J. Zhang, Z., Aguirre, S. D., Pelton, R., Li, Y., Filipe, C. D. M. (2014). Turning Tryptophanase into Smell-Generating Biosensors. Angew. Chem. Int. Ed. 53, 2620-2. doi: 10.1002/anie.201309684.

130. Ghazi, Z., Fowler, C. C., Li, Y. (2014) Artificial Riboswitch Selection: A FACS-Based Approach. Methods Mol. Biol. 1111, 57-75. doi: 10.1007/978-1-62703-755-6_5.

129. Fowler C. C., Li, Y. (2014). Construction and application of riboswitch-based sensors that detect metabolites within bacterial cells. Methods Mol. Biol. 1103, 177-97.

128. Lu, D., Liu, L., Li, F., Shuang, S., Li, Y., Choi, M. M., Dong, C. (2014). Lysozyme-stabilized gold nanoclusters as a novel fluorescence probe for cyanide recognition. Spectrochim Acta A Mol Biomol Spectrosc. 121, 77-80.

127. Lau, P. S. & Li, Y. (2014). Exploration of Structure-Switching in the Design of Aptamer Biosensors. Adv. Biochem. Eng. Biotechnol. 140, 69-92.

126. Li, Y. (2013) Evolving Wonder-RNAs in a Test Tube. J Mol Evol. 77, 197-198.

125. Bian, W., Ma, J., Guo, W., Lu, D., Fan, M., Wei, Y., Li, Y., Shuang, S., Choi, M. M. (2013). Phosphorescence detection of L-ascorbic acid with surface-attached N-acetyl-L-cysteine and L-cysteine Mn doped ZnS quantum dots. Talanta. 116, 794-800

124. Fowler, C. C., Sugiman-Marangos, S., Junop, M. S., Brown, E. D., Li, Y. (2013). Exploring Intermolecular Interactions of a Substrate-Binding Protein Using a Riboswitch-Based Sensor. Chem. Biol. 20, 1502-1512.

123. Aguirre, S. D., Ali, M. M., Salena, B. J. & Li, Y. (2013). A Sensitive DNA Enzyme-Based Fluorescent Assay for Bacterial Detection. Biomolecules 3, 563-577.

122. McManus, S. A., Li, Y. (2013). Assessing the Amount of Quadruplex Structures Present within Diguanine Repeat Libraries. Plos ONE. 8, e64131

121. Bian, W., Ma, J., Liu, Q., Wei, Y., Li, Y., Dong, C., Shuang, S. (2013). A novel phosphorescence sensor for Co2+ ion based on Mn-doped ZnS quantum dots. Luminescence. 2013: doi: 10.1002/bio.2520.

120. McManus, S. A., Li, Y. (2013). Turning a Kinase Deoxyribozyme into a Sensor. J. Am. Chem. Soc. 135, 7181-7186.

119. Lau, P. S., Lai, C. K., Li, Y. (2013). Structure-Switching RNA Aptamers with a Quality Control Element. ChemBioChem. 14, 987-992.

118. Mok, W. W. K., Li, Y. (2013). A Highly Efficient Molecular Cloning Platform that Utilizes a Small Bacterial Toxin Gene. ChemBioChem. 14, 733-738. Most accessed paper in 2013.

117. Kuwahara, M., Li, Y., Rozners, E., Murakami, H. (2013). Artificially Created Nucleic Acids and Peptides/Proteins in Chemical Biology. J. Nucleic Acids. 2013:219263. doi: 10.1155/2013/219263.

116. Tram, K., Kanda, P., Li, Y. (2012). Lighting Up RNA-cleaving DNAzymes for Biosensing. J Nucleic Acids. 2012:958683. doi: 10.1155/2012/958683.

115. Wang, G.-N., Lau, P. S., Li, Y., Ye, X.-S. (2012). Synthesis and evaluation of glucosamine-6-phosphate analogues as activators of glmS riboswitch. Tetrahedron, 68, 9405-9412.

114. Carrasquilla, C., Lau, P. S., Li, Y., Brennan, J. D. (2012). Stabilizing structure-switching signaling RNA aptamers by entrapment in sol-gel derived materials for solid-phase assays. J. Am. Chem. Soc. 134, 10998-11005

113. Aguirre, S. D., Ali, M. M., Kanda, P., Li, Y. (2012). Detection of bacteria using fluorogenic DNAzymes. Journal of Visualized Experiments. 63, pii: 3961. doi: 10.3791/3961

112. Hossain, S. M. Z., Ozimok, C., Ali, M. M., Aguirre, S. D., Li, Y. and Brennan, J. D. (2012). Multiplexed paper test strip for quantitative bacterial detection. Anal. Bioanal. Chem. 403(6):1567-76.

111. Ali, M. M., Aguirre, S. D., Mok, W. W. K., & Li, Y. (2012). Developing fluorogenic RNA-cleaving DNAzymes for biosensing applications. Methods Mol. Biol. 848, 395-418.

110. Carrasquilla, C., Yao, X., Xu, C.-Q., Li, Y. and Brennan, J. D. (2011). Enhancing Sensitivity and Selectivity of Long-Period Grating Sensors using Structure-Switching Aptamers Bound to Gold-Doped Macroporous Silica Coatings for Small Molecule Detection. Biosensors and Bioelectronics. Submitted.

109. Ali, M. M., Aguirre, S. D., Mok, W. W. K, & Li, Y. (2011). Developing Fluorogenic RNA-cleaving DNAzymes for Biosensing Applications. Methods in Molecular Biology. Submitted.

108. Lam, J. C. F., Kwan, S. O., & Li, Y. (2011). Characterization of Non-8-17 Sequences Uncovers Structurally Diverse RNA-cleaving Deoxyribozymes. Molecular BioSystems. In press. [link]

107. Xu, Y., Pharand, L., Wen, Q., Gonzaga, F., Ali, M. M., Li, Y., Filipe, C. D. M., & Pelton, R. (2011). Controlling Biotinylation of Microgels and Modeling Streptavidin Uptake. Colloid and Polymer Science. 289, 659-666. [link]

106. Ali, M. M., Aguirre, S. D., Lazim, H., & Li, Y. (2011). Fluorogenic DNAzyme Probes as Bacterial Indicators. Angewandte Chemie International Edition. 50, 3751-4. [link]

Featured in: [Science Daily] [CTS TV News] [McMaster Daily News] [Internetchemistry.com] [PhysOrg.com] [Innovations Report]

105. Carrasquilla, C., Li, Y., & Brennan, J. D. (2011). Surface Immobilization of Structure-Switching DNA Aptamers on Macroporous Sol-Gel-Derived Films for Solid-Phase Biosensing Applications. Analytical Chemistry. 83, 957-965. [link]

104. Ali, M. M, Kanda, P., Aguirre, S. D., & Li, Y. (2011). Modulation of DNA-Modified Gold-Nanoparticle Stability in Salt with Concatemeric Single-Stranded DNAs for Colorimetric Bioassay Development. Chemistry – A European Journal. 17, 2052-2056. [link]

103. Lau, P. S. & Li, Y. (2011). Functional nucleic acids as molecular recognition elements for small organic and biological molecules. Curr. Org. Chem. 15, 557-575. Invited review. [link]

102. Mok, W. W. K., Patel, N., & Li, Y. (2010). Decoding Toxicity: Deducing the Sequence Requirements of IbsC, a Type I Toxin in Escherichia coli.Journal of Biological Chemistry. 285: 41627-36. [link]

101. Lau, P. S., Coombes, B. K., & Li, Y. (2010). A General Approach to the Construction of Structure-Switching Reporters from RNA Aptamers.Angew. Chem. Int. Ed. 49, 7938-7942. [link]

100. McManus, S. A., & Li, Y. (2010). The Structural Diversity of Deoxyribozymes. Molecules. 15, 6269-6284. Review. [link]

99. Wang, B., Cao, L., Chiuman, W., Li, Y. & Xi, Z. (2010). Probing the function of nucleotides in the catalytic cores of the 8-17 and 10-23 DNAzymes by abasic nucleotide and C3 spacer substitutions. Biochemistry 49, 7553-7562. [link]

98. Lam, J. & Li, Y. (2010). Influence of Cleavage Site on Global Folding of an RNA-Cleaving DNAzyme. ChemBioChem. 11, 1710 – 1719. [link]

97. Fowler, C. C., Brown, E. D. & Li, Y. (2010). Using a riboswitch sensor to monitor coenzyme B12 metabolism and transport in E. coli. Chem. Biol. 17, 756-765. [link]

96. Lam, J. C., Withers, J. B. & Li, Y. (2010). A complex RNA-cleaving DNAzyme that can efficiently cleave a pyrimidine-pyrimidine junction. J. Mol. Biol. 400, 689-701. [link]

95. Budz, H. A., Ali, M. M., Li, Y. & LaPierre, R. R. (2010). Photoluminescence Model for a Hybrid Aptamer-GaAs Optical Biosensor. J. Appl. Phys. 107, 104702 (1-9). [link]

94. Schlosser, K. & Li, Y. (2010). A versatile endoribonuclease made of DNA: characteristics and applications of the 8-17 DNAzyme. ChemBioChem. 11, 866-879. Review. [link]

93. Ali, M. M, Aguirre, S. D., Xu,Y., Filipe, C. D. M., Pelton, R. & Li, Y. (2009). Detection of DNA Using Bioactive Paper Strips. Chem. Comm. 2009, 6640-2. [link]

92. Kandadai, S. A., Mok, W. W. K., Ali, M. M., & Li, Y. (2009). Characterization and Optimization of an RNA-Cleaving Deoxyribozyme Active at pH 5. Biochemistry 48, 7383-91. [link]

91. Schlosser, K., Lam, J. & Li, Y. (2009). A genotype-to-phenotype map of in vitro selected RNA- cleaving DNAzymes: Implications for accessing the target phenotype. Nucleic Acids Res. 37, 3545-57. [link]

90. Ali, M. M., Imoto, S., Li, Y., Sasaki, S. & Nagatsugi. (2009). Incorporation of an inducible nucleotide analog into DNA by DNA polymerases.Bioorg. Med. Chem. 17, 2859-63. [link]

89. Nakamura, I., Shi, A., Nutiu, R., Yu, J. M. Y. & Li, Y. (2009). Kinetic modeling of designed signaling DNA aptamers. Physical Review E. 79: 031906. [link]

88. Ali, M. M. & Li, Y. (2009). Colorimetric sensing using allosteric DNAzyme-coupled rolling circle amplification and a peptide nucleic acid-organic dye probe. Angew. Chem. Int. Ed. 48, 3512-3515. [link]

87. Schlosser, K. & Li, Y. (2009). Biologically inspired synthetic enzymes made from DNA. Chem. Biol. Invited review. 16, 311-22. [link]

86. Schlosser, K. & Li, Y. (2009). DNAzyme-mediated catalysis with only guanosine and cytidine nucleotides. Nucleic Acids Res. 37, 413-420. [link]

85. Mok, W. W. K., Navani, N. K. Barker, C., Sawchyn, B. L., Gu, J., Pathania, R., Zhu, R. D., Brown, E. D. & Li, Y. (2009). Identification of a toxic peptide through bidirectional expression of small RNAs. ChemBioChem. 10, 238-241. [link]

84. Mok, W. W. K. & Li, Y. (2008). Recent Progress in Nucleic Acid Aptamer-Based Biosensors and Bioassays. Sensors. 8, 7050-7084. Review.[link]

83. Zhao, W., Ali, M. M., Aguirre, S., Brook, M. A. & Li, Y. (2008). Paper-based Bioassays Using Gold Nanoparticle Colorimetric Probes. Anal. Chem. 80, 8431-8437. [link]

82. Sun, G., Fan, J., Wang, Z., Li, Y. (2008). A DNA-Catalyzed Aldol Reaction in Water. SynLett. 2008, 16, 2491-2494. [link]

81. Zhao, W., Brook, M. A. & Li, Y. (2008). Design of gold nanoparticle-based colorimetric biosensing assays. ChemBioChem. 9, 2363-2371. Review. [link]

80. Schlosser, K., Gu, J., Lam, J. C. F. & Li, Y. (2008). In vitro selection of small RNA-cleaving deoxyribozymes that cleave pyrimidine-pyrimidine junctions. Nucleic Acids Res. 36, 4768- 4777. [link]

79. Fan, J., Sun, G., Wan, C., Wang, Z. & Li, Y. (2008). Investigation of DNA as a Catalyst for Henry Reaction in Water. Chem. Comm. 2008, 3792-3794. [link]

78. Li, Y. (2008). Chemical Biology meets Systems Biology. Biochem. Cell Biol. 86, vii-viii. [link]

77. Fowler, C. C., Brown, E. D. & Li, Y. (2008). A FACS-Based Approach to Engineering Artificial Riboswitches. ChemBioChem. 9, 1906-1911. [link]

76. Zhao, W., Ali, M. M., Brook, M. A., & Li, Y. (2008). Rolling Circle Amplification: New Applications in Nanotechnology and Functional Nucleic Acid-Based Biodetection. Angew. Chem. Int. Ed. 47, 6330-6337. Review. [link]

75. Zhao, W., Lam, J. C. F, Chiuman, W., Brook, M. A. & Li, Y. (2008). Enzymatic cleavage of nucleic acid on gold nanoparticle: a generic platform for facile colorimetric biosensors. Small. 4, 810-816. [link]

74. Zhao, W., Chiuman W., Lam, J. C. F, McManus, S. A., Chen, W., Cui, Y., Pelton, R., Brook, M. A. & Li, Y. (2008). DNA Aptamer Folding on Gold Nanoparticle: from Colloid Chemistry to Biosensors. J. Am. Chem. Soc. 130, 3610-3618. [link]

73. Su, S., Ali, M. M., Filipe, C. D. M., Li, Y. & Pelton, R. (2008). Microgel-based Inks for Paper- supported Biosensing Applications.Biomacromolecules. 9, 935-941. [link]

72. Schlosser, K., & Li, Y. (2008). Sequence-function relationships provide new insight into the cleavage site selectivity of the 8-17 RNA-cleaving deoxyribozyme. Nucleic Acids Res. 36, 1472-1481. [link]

71. McManus, S. A. & Li, Y. (2008). A Deoxyribozyme with a Novel Guanine Quartet-Helix Pseudoknot Structure. J. Mol. Biol. 375: 960-968. [link]

70. Yang, J., Sandhu, P., Liang, W, Xu, C.-Q.,. & Li, Y. (2007). Label-Free Fiber Optic Biosensors with Enhanced Sensitivity. IEEE J. Selected Topics in Quantum Electronics. 13, 1691-1696. [link]

69. Schlosser K. & Li, Y. (2007). Understanding DNA-based catalysis one molecule at a time. Nat. Chem. Biol. 3, 753-754. News & Views. [link]

68. Chiuman, W. & Li, Y. (2007). Simple fluorescent sensors engineered with catalytic DNA MgZ based on a non-allosteric design. PloS ONE. 2, e1224. [link]

67. Allali-Hassani, A., Pereira, M. P., Navani, N. K., Brown, E. D. & Li, Y. (2007). Isolation of DNA aptamers for CDP-ribitol synthase and characterization of their inhibitory and structural properties. ChemBioChem. 8, 2052-2057. [link]

66. Ali, M. M., Su, S., Filipe, C. D. M., Pelton, R. & Li, Y. (2007). Enzymatic Manipulations of DNA Oligonucleotides on Microgel: Towards Development of DNA-Microgel Biosensors. Chem. Comm. 2007, 4459-4461. [link] (Highlighted in the chemical biology news of Royal Chemical Society, 2007, 2, B83).

65. Fowler, C. C. & Li, Y. (2007). Aptamers and small Molecules play tug of war. Chem. Biol. 14, 736-738. Preview. [link]

64. Zhao, W., Chiuman, W., Lam, J. C. F, Brook, M. A. & Li, Y. (2007). Simple and rapid colorimetric enzyme sensing assays using non-crosslinling gold nanoparticle aggregation. Chem. Comm. 2007, 3729 – 3731. [link]

63. Zhao, W., Gonzaga, F., Li, Y. & Brook, M. A. (2007). Highly Stabilized Nucleotide-capped Small Gold Nanoparticles with Tunable Size. Adv. Mater. 19, 1766-1771. [link]

62. Zhao, W., Chiuman, W., Brook, M. A. & Li, Y. (2007). Simple and Rapid Colorimetric Biosensors Based on DNA Aptamer and Non-crosslinking Gold Nanoparticle Aggregation”. ChemBioChem. 8, 727-731. [link]

61. Ali, M. M., Kandadai, S. & Li, Y. (2007). Characterization of pH3DZ1—an RNA-Cleaving Deoxyribozyme with Optimal Activity at pH 3. Can. J. Chem. 85, 261-273. [link]

60. Craney, Ar., Hohenauer, T., Xu, Y., Kumar, N., Li, Y. & Nodwell, J. (2007). A synthetic luxCDABE gene cluster optimized for expression in high-GC bacteria. Nucleic Acids Research. 35, e46. [link]

59. Shen, Y., Mackey, G., Rupcich, N., Gloster, D., Chiuman, W., Li, Y. and Brennan, J. D. (2007). Entrapment of Fluorescence-Signaling DNA Enzymes in Sol-Gel Derived Materials for Metal Ion Sensing. Anal. Chem. 79, 3494-3503. [link]

58. Yang, J., Yang, L., Xu, C-Q., Huang, W. and Li, Y. (2007). Optimization of cladding structure modified long-period grating refractive index sensors. Journal of Lightwave Technology. 25, 372-380. [link]

57. McManus, S., Li, Y. (2007). Multiple Occurrences of an Efficient Self-Phosphorylating Deoxyribozyme Motif. Biochemistry 46, 2198-2204. [link]

56. Chiuman, W. & Li, Y. (2007). Efficient Signaling Platforms Built from a Small Catalytic DNA and Doubly Labeled Fluorogenic Substrates. Nucleic Acids Research. 35, 401-405. [link]

55. Su, S., Nutiu, N., Filipe, C. D. M., Li, Y. & Pelton, R. (2007). Adsorption and Covalent Coupling of ATP-Binding DNA Aptamers onto Cellulose.Langmuir. 23, 1300-1302. [link]

54. Shen, Y., Chiuman, W., Brennan, J. D. & Li, Y. (2006). Catalytic and signaling properties of trans-acting pH6DZ1, an RNA-cleaving and fluorescence-signaling deoxyribozyme with a four-way junction structure. ChemBioChem. 7, 1343-1348. [link]

53. Chiuman, W. & Li, Y. (2006). Evolution of high-branching deoxyribozymes from a catalytic DNA with a three-way junction. Chem. Biol. 13, 1061-1069. [link]

52. Yang, J., Yang, L., Xu, C.-Q., Xu, C., Huang, W. & Li, Y. (2006) Long-period grating refractive index sensor with a modified cladding structure for large operational range and high sensitivity. Applied Optics. 45, 6142-6147. [link]

51. Elowe, N. H., Nutiu, R., Allali-Hassani, A., Cechetto, J. D., Hughes, D. W., Li, Y. & Brown, E. D. (2006). Screening made simple for a difficult target with a signaling aptamer for deaminase activity. Angew. Chem. Int. Ed. 45, 5648-5652. [link]

50. Zhao, W., Gao, Y., Brook, M. A. & Li, Y. (2006) Wrapping Single-Walled Carbon Nanotubes with Long Single-Stranded DNA Molecules Produced by Rolling Circle Amplification. Chem. Comm. 2006, 3582 –3584. 45. [link]

49. Zhao, W., Gao, Y., Kandadai, S. A., Brook, M. A. & Li, Y. (2006) DNA Polymerization on Gold Nanoparticles via Rolling Circle Amplification: Towards Novel Scaffold for Three- Dimensional Periodical Nanoassembly. Angew. Chem. Int. Ed. 45, 2409-2413. [link]

48. Navani, N. K. & Li, Y. (2006) Nucleic acid aptamers and enzymes as sensors. Curr. Opin. Chem. Biol. 10, 272-281. Review. [link]

47. Kandadai, S. A., Chiuman, W. & Li, Y. (2006). Phosphoester-transfer mechanism of an RNA- cleaving acidic deoxyribozyme revealed by radioactivity tracking and enzymatic digestion. Chem. Comm. 2006, 2359-2361. [link]

46. Schlosser, K., Lam, J. & Li, Y. (2006). Characterization of long RNA-cleaving deoxyribozymes with short catalytic cores: The effect of excess sequence elements on the outcome of in vitro selection. Nucleic acids Res. 34, 2445-2454. [link]

45. Rupcich, N., Nutiu, R., Li, Y. & Brennan, J. D. (2006). Solid-Phase Enzyme Activity Assay Utilizing an Entrapped Fluorescence-Signaling DNA Aptamer. Angew. Chem. Int. Ed. 45, 3295-3299. [link]

44. Chiuman, W. & Li, Y. (2006). Revitalization of six abandoned catalytic DNA species reveals a common three-way junction framework and diverse catalytic cores. J. Mol. Biol. 357, 748–754. [link]

43. Rupcich, N., Chiuman, W., Nutiu, R., Mei, S., Flora, K. K., Li, Y. & Brennan, J. D. (2006). Quenching of Fluorophore-labeled DNA Oligonucleotides by Divalent Metal Ions: Implications for Selection, Design and Applications of Signaling Aptamers and Signaling Deoxyribozymes. J. Am. Chem. Soc. 2006, 128, 780-790. [link]

42. Kandadai, S. & Li, Y. (2006). Characterization of a catalytically efficient acidic RNA-cleaving deoxyribozyme. Nucleic Acids Res. 33, 7164–7175.[link]

41. Jin, J., Achenbach, J. C., Zhu, S. & Li, Y. (2005). Complexation of Well-Controlled Low- Molecular-Weight Polyelectrolytes with Antisense Oligonucleotides. Colloid and Polymer Science. 283, 1197 – 1205. [link]

40. Nutiu, R. & Li, Y. (2005). Aptamers with fluorescence-signaling properties. Methods. 37, 16- 25. Review. [link]

39. Schlosser, K. & Li, Y. (2005). Diverse evolutionary trajectories characterize a community of RNA-cleaving deoxyribozymes: A case study into population dynamics of in vitro selection. J. Mol. Evol. 61, 192-206. [link]

38. Shen, Y., Brennan, J. D. & Li, Y. (2005). Characterizing the secondary structure and identifying functionally essential nucleotides of pH6DZ1, a fluorescence-signaling and RNA-cleaving deoxyribozyme. Biochemistry 44, 12066-12076. [link]

37. Nutiu, R. & Li, Y. (2005). A DNA-Protein Nanoengine for ‘On-Demand’ Release and Precise Delivery of Molecules. Angew. Chem. Int. Ed. 44, 5464-5467. [link]

36. Rupcich, N., Nutiu, R. & Li, Y., Brennan, J. D. (2005). Entrapment of Fluorescent signaling aptamers in Sol-Gel Derived Silica. Anal. Chem. 77, 4300-4307. [link]

35. Achenbach, J. C., Nutiu, R & Li, Y. (2005). Structure-switching allosteric deoxyribozymes. Analytica Chimica Acta. 534, 41-51. [link]

34. Achenbach, J. C., Jeffries, G., McManus, S., Billen, L. P. & Li, Y. (2005). Secondary-structure characterization of two proficient kinase deoxyribozymes. Biochemistry 44, 3765-3774. [link]

33. Krylova, S. M., Musheeva. M., Nutiu, R., Li, Y., Lee, G. & Krylov, S. N. (2005). Tau protein binds both double-stranded and single-stranded DNA – the proof obtained with nonequilibrium capillary electrophoresis of equilibrium mixtures. FEBS Lett. 579, 1371-1375. [link]

32. Nutiu, R. & Li, Y. (2005). In vitro selection of structure-switching signaling aptamers. Angew. Chem. Int. Ed. 44, 1061-1065. [link]

31. Billen, L. P. & Li, Y. (2004). Synthesis and characterization of topologically linked single- stranded DNA rings. Bioorg. Chem. 32, 582-598. [link]

30. Nutiu, R., Mei, S. H. J., Liu, Z. & Li, Y. (2004). Engineering DNA aptamers and DNA enzymes with fluorescence-signaling properties. Pure & Applied Chemistry. 76, 1547-1561. Review. [link]

29. Achenbach, J. C., Chiuman, W., Cruz, R. P. G. & Li, Y. (2004) DNAzymes: From Creation In Vitro to Application In Vivo. Current Pharmaceutical Biotechnology. 5, 321-336. Review. [link]

28. Nutiu, R. Yu, J. M. Y. & Li, Y. (2004). An aptamer-based fluorescence assay for monitoring enzymatic activity and enzyme inhibitor screening.ChemBioChem. 5, 1139-1144. [link]

27. Schlosser, K. & Li, Y. (2004). Tracing sequence diversity change of RNA-cleaving deoxyribozymes under increasing selection pressure during in vitro selection. Biochemistry. 43, 9695-9707. [link]

26. Sreedhara, A., Li, Y. & Breaker, R. R. (2004). Ligating DNA with DNA. J. Am. Chem. Soc. 126, 3454-3460. [link]

25. Nutiu, R. & Li, Y. (2004). Structure-Switching Signaling Aptamers: Transducing molecular recognition into fluorescence signaling. Chemistry-A European Journal. 10, 1868-1876. Review. [link]

24. Cruz, R. P. G., Withers, J. S. & Li, Y. (2004). Dinucleotide Junction cleavage versatility of 8- 17 deoxyribozyme. Chem. Biol. 11, 57-67. [link]

23. Schlosser, K., Mei, S. H. J. & Li, Y. (2003). Catalytic DNAs as reporter molecules. Recent Res. Develop. Chem. 1, 143-161. [link]

22. Liu, Z., Mei, S. H. J., Brennan, J. D. & Li, Y. (2003). Assemblage of signalling DNA enzymes with intriguing metal specificity and pH dependences. J. Am. Chem. Soc. 125, 7539-7545. [link]

21. Nutiu, R. & Li, Y. (2003). Structure-switching signaling aptamers. J. Am. Chem. Soc., 125, 4771-4778. [link]

20. Berezovski, M., Nutiu, R., Li, Y. & Krylov, S. N. (2003). Affinity analysis of a protein-aptamer complex using non-equilibrium capillary electrophoresis of equilibrium mixtures. Anal. Chem. 75, 1382-1386. [link]

19. Mei, S. H. J., Liu, Z., Brennan, J. D. & Li, Y. (2003). An efficient RNA-cleaving DNA enzyme that synchronizes catalysis with fluorescence signaling. J. Am. Chem. Soc. 125, 412-420. [link]

18. Chiuman, W. & Li, Y. (2002). Making AppDNA using T4 DNA ligase. Bioorg. Chem. 30, 332- 349. [link]

17. Nutiu, R. & Li, Y. (2002). Tripartite Molecular beacons. Nucleic Acids. Res. 30, e94. [link]

16. Wang, W., Billen, L. P. & Li, Y. (2002). Sequence diversity, metal specificity and catalytic proficiency of metal-dependent deoxyribozymes.Chem. Biol. 9, 507-517. [link]

15. Li, Y. & Breaker, R. R. (2001). In vitro selection of kinase and ligase deoxyribozymes. Methods 23, 179-190. Review. [link]

14. Li, Y., Liu, Y. & Breaker, R. R. (2000). Capping DNA with DNA. Biochemistry 39, 3106- 3114. [link]

13. Li, Y. & Breaker, R. R. (1999). Deoxyribozymes: New players in the ancient games of biocatalysis. Curr. Opin. Struct. Biol. 9, 315-323. Review.[link]

12. Li, Y. & Breaker, R. R. (1999). Phosphorylating DNA with DNA. Proc. Natl. Acad. Sci. U. S. A. 96, 2746-2751. [link]

11. Li, Y. & Breaker, R. R. (1999). Kinetics of RNA degradation by specific base catalysis of transesterification involving the 2′-hydroxyl group. J. Am. Chem. Soc. 121, 5364-5372. [link]

10. Travascio, P., Li, Y. & Sen, D. (1998). DNA-enhanced peroxidase activity of DNA aptamer- hemin complex. Chem. Biol. 5, 505-517. [link]

9. Li, Y. & Sen, D. (1998). The modus operandi of a DNA enzyme: Enhancement of substrate basicity. Chem. Biol. 5, 1-12. [link]

8. Li, Y. & Sen, D. (1997). Towards an efficient DNAzyme. Biochemistry 36, 5589-5599. [link]

7. Li, Y. & Sen, D. (1996). A catalytic DNA for porphyrin metallation. Nat. Struct. Biol. 3, 743- 747. [link]

6. Li, Y., Geyer, C. R. & Sen, D. (1996). Recognition of anionic porphyrins by DNA aptamers. Biochemistry 35, 6911-6922. [link]

5. Li, Y. & Wang, H. (1992). Studies on bromination of phenol by dioxane-dibromide. Journal of Chemical Reagents 14, 50-51.

4. Li, Y. & Zhou, C. (1991). Synthesis and Bioactivity of Some Novel Non-Ester Pyrethroids (I). Chemical Journal of Chinese Universities 12, 479-481.

3. Li, Y. & Zhou, C. (1991). Synthesis and bioactivity of some novel non-ester pyrethroids (II). Journal of Applied Chemistry 8, 63-66.

2. Li, Y. & Zhou, C. (1990). A new synthetic route for alkane pyrethroids. Journal of Pesticide Science 187, 39-43.

1. Li, Y. & Zhou, C. (1990). Synthesis of p-fluoro-m-phenoxytoluene. Journal of Pesticide Science 183, 17-20.