Zambrano, R.A.I., Hernandez-Perez, C., Takahashi, M.K., “RNA structure prediction, analysis, and design: an introduction to web-based tools,” Methods Mol Biol., 2022, 2518, 253-269. DOI: 10.1007/978-1-0716-2421-0_15

Takahashi, M.K.*, Tan, X.*, Dy, A.J.*, “Cell-free paper-based analysis of gut microbiota and host biomarkers,” Methods Mol Biol., 2022, 2433, 351-374. DOI: 10.1007/978-1-0716-1998-8_22

Hunt, J.P., Zhao, E.L., Free, T.J., Soltani, M., Warr, C.A., Benedict, A.B., Takahashi, M.K., Griffitts, J.S., Pitt, W.G., Bundy, B.C., “Towards detection of SARS-CoV-2 RNA in human saliva: A paper-based cell-free toehold switch biosensor with a visual bioluminescent output,” N Biotechnology, 2022, 66, 53-60. DOI: 10.1016/j.nbt.2021.09.002

Lopatkin, A.J, Stokes, J.M., Zheng, E.J., Yang, J.H., Takahashi, M.K., You, L, and Collins, J.J., “Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate,” Nature Microbiology, 2019. DOI: 10.1038/s41564-019-0536-0

Takahashi, M.K.*, Tan, X.*, Dy, A.J.*, Braff, D., Furuta, Y., Akana, R.T., Donghia, N., Ananthakrishnan, A., and Collins, J.J., “A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers,” Nature Communications, 2018. DOI: 10.1038/s41467-018-05864-4 

Huang, A.*, Nguyen, P.Q.*, Stark, J.C.*, Takahashi, M.K., Donghia, N., Ferrante, T., Dy, A.J., Hsu, K.J., Dubner, R.S., Pardee, K., Jewett, M.C., and Collins, J.J., “BioBits Explorer: A modular synthetic biology education kit,” Science Advances, 2018. DOI: 10.1126/sciadv.aat5105

Hu, C.Y.*, Takahashi, M.K.*, Zhang, Y., and Lucks, J.B., “Engineering a functional small RNA negative autoregulation network with model-guided design,” ACS Synthetic Biology, 2018. DOI: 10.1021/acssynbio.7b00440

Pardee, K.*, Green, A.A.*, Takahashi, M.K.*, Braff, D.*, Lambert, G.*, Lee, J.W., Ferrante, T., Ma, D., Donghia, N., Fan, M., Daringer, N.M., Bosch, I., Dudley, D.M., O’Connor, D.H., Gehrke, L., and Collins, J.J., “Rapid, low-cost detection of Zika virus using programmable biomolecular components,” Cell, 2016. DOI: 10.1016/j.cell.2016.04.059

Takahashi, M.K., Watters, K.E., Gasper, P.M., Abbott, T.R., Carlson, P.D., Chen, A.A., and Lucks, J.B., “Using in-cell SHAPE-Seq and simulations to probe structure-function design principles of RNA transcription regulators,” RNA, 2016. DOI: 10.1261/rna.054916.115

Takahashi, M.K.*, Hayes, C.A.*, Chappell, J., Sun, Z.Z., Murray, R.M., Noireaux, V., and Lucks, J.B., “Characterizing and prototyping genetic networks with cell-free transcription-translation reactions,” Methods, 2015. DOI: 10.1016/j.ymeth.2015.05.020

Chappell, J., Watters, K.E., Takahashi, M.K., and Lucks, J.B., “A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future,” Current Opinion in Chemical Biology, 2015. DOI: 10.1016/j.cbpa.2015.05.018

Chappell, J., Takahashi, M.K., and Lucks, J.B., “Creating small transcription activating RNAs (STARs),” Nature Chemical Biology, 2015.  DOI: 10.1038/NCHEMBIO.1737

Takahashi, M.K., Chappell, J., Hayes, C.A., Sun, Z.Z., Kim, J., Singhal, V., Spring, K.J., Al-Khabouri, S., Fall, C.P., Noireaux, V., Murray, R.M., and Lucks, J.B., “Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription-translation (TX-TL) systems,” ACS Synthetic Biology, 2015. DOI: 10.1021/sb400206c

Chappell, J., Takahashi, M.K., Meyer, S., Loughrey, D., Watters, K.E., and Lucks, J.B., “The centrality of RNA for engineering gene expression,” Biotechnology Journal, 2013. DOI: 10.1002/biot.201300018

Takahashi, M.K., and Lucks, J.B., “A modular strategy for engineering orthogonal chimeric RNA transcription regulators,” Nucleic Acids Research, 2013. DOI: 10.1093/nar/gkt452

* Indicates co-first author